From 127be4842ab0a56c7ef63937759ff1e1cbff6ba7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 6 Feb 2020 13:21:04 -0500
Subject: [PATCH 01/96] Automatically resolve and add static-safe mappings for
 client-based images.  This is safe, and we might as well just automate/force
 it here.  People can always add additional ones, of course, but this ensures
 galaxy internal static files are resolvable.

---
 scripts/get_uwsgi_args.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index 80eae973a68..999e9d2c617 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -121,6 +121,8 @@ def _get_uwsgi_args(cliargs, kwargs):
         if hmr_server.lower() in ['1', 'true', 'default']:
             hmr_server = "http:127.0.0.1:8081"
         __add_arg(args, 'route', '^/static/scripts/bundled/ {hmr_server}'.format(hmr_server=hmr_server))
+    # We always want to append client/galaxy/images as static-safe.
+    __add_arg(args, 'static-safe', '{here}/client/galaxy/images'.format(here=os.getcwd()))
 
     for arg in DEFAULT_ARGS['_all_'] + DEFAULT_ARGS[cliargs.app]:
         if not __arg_set(arg, uwsgi_kwargs):

From e7a2e9a4403ae5da5540a8549d2f3d7740f1062d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 6 Feb 2020 13:23:42 -0500
Subject: [PATCH 02/96] With it configured to always set static-safe, this is
 no longer necessary

---
 scripts/get_uwsgi_args.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index 999e9d2c617..093c2b1b72a 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -94,7 +94,6 @@ def _get_uwsgi_args(cliargs, kwargs):
         'static-map': ('/static/style={here}/static/style/blue'.format(here=os.getcwd()),
                        '/static={here}/static'.format(here=os.getcwd()),
                        '/favicon.ico={here}/static/favicon.ico'.format(here=os.getcwd())),
-        'static-safe': ('{here}/client/galaxy/images'.format(here=os.getcwd())),
         'die-on-term': True,
         'enable-threads': True,
         'hook-master-start': ('unix_signal:2 gracefully_kill_them_all',

From 4834b7535f6cc21f93b0035c3b5819549a26262c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 6 Feb 2020 13:27:33 -0500
Subject: [PATCH 03/96] Drop static-safe from DEFAULT_ARGS, relying on an
 explicit add now.

---
 scripts/get_uwsgi_args.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index 093c2b1b72a..d8a803ac26a 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -23,7 +23,7 @@ ALIASES = {
     'module': ('mount',),   # mount is not actually an alias for module, but we don't want to set module if mount is set
 }
 DEFAULT_ARGS = {
-    '_all_': ('pythonpath', 'threads', 'buffer-size', 'http', 'static-map', 'static-safe', 'die-on-term', 'hook-master-start', 'enable-threads', 'umask'),
+    '_all_': ('pythonpath', 'threads', 'buffer-size', 'http', 'static-map', 'die-on-term', 'hook-master-start', 'enable-threads', 'umask'),
     'galaxy': ('py-call-osafterfork',),
     'reports': (),
     'tool_shed': ('cron',),

From 21a0324887b3b49e1463373a83124ab51fd43320 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 13:05:14 +0100
Subject: [PATCH 04/96] Add requirements to all converters that use bgzip.py

---
 lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml  | 6 +++++-
 .../datatypes/converters/encodepeak_to_bgzip_converter.xml  | 6 +++++-
 lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml  | 6 +++++-
 .../datatypes/converters/interval_to_bgzip_converter.xml    | 6 +++++-
 lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml  | 6 +++++-
 .../datatypes/converters/vcf_to_vcf_bgzip_converter.xml     | 6 +++++-
 6 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
index 08d91cddf72..c19d371f019 100644
--- a/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_bed_to_bgzip_0" name="Convert BED to BGZIP" version="1.0.0" hidden="true">
+<tool id="CONVERTER_bed_to_bgzip_0" name="Convert BED to BGZIP" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
+    </requirements>
     <command>python '$__tool_directory__/bgzip.py' -P bed '$input1' '$output1'</command>
     <inputs>
         <param format="bed" name="input1" type="data" label="Choose BED file"/>
diff --git a/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
index babbe100a48..15518840912 100644
--- a/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_encodepeak_to_bgzip_0" name="Convert ENCODEPeak to BGZIP" version="1.0.0" hidden="true">
+<tool id="CONVERTER_encodepeak_to_bgzip_0" name="Convert ENCODEPeak to BGZIP" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/bgzip.py'
         -c ${input1.metadata.chromCol}
diff --git a/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
index f26f8049bb8..412a6553caa 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_gff_to_bgzip_0" name="Convert GFF to BGZIP" version="1.0.0" hidden="true">
+<tool id="CONVERTER_gff_to_bgzip_0" name="Convert GFF to BGZIP" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
+    </requirements>
     <command>python '$__tool_directory__/bgzip.py' -P gff '$input1' '$output1'</command>
     <inputs>
         <param format="gff" name="input1" type="data" label="Choose GFF file"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 615170f893a..b630dac23d0 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.0" hidden="true">
+<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/bgzip.py'
         -c ${input1.metadata.chromCol}
diff --git a/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
index 79a09003382..7986ce2efe6 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_vcf_to_bgzip_0" name="Convert VCF to BGZIP" version="1.0.0" hidden="true">
+<tool id="CONVERTER_vcf_to_bgzip_0" name="Convert VCF to BGZIP" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
+    </requirements>
     <command>python '$__tool_directory__/bgzip.py' -P vcf '$input1' '$output1'</command>
     <inputs>
         <param format="vcf" name="input1" type="data" label="Choose Vcf file"/>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
index 6b015752ca9..daa84accc25 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.1" hidden="true">
+<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.2" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
+    </requirements>
     <command>python '$__tool_directory__/vcf_to_vcf_bgzip.py' '$input1' '$output1'</command>
     <inputs>
         <param format="vcf" name="input1" type="data" label="Choose Vcf file"/>

From 113b01085ab3a5121b306328ea40a4cb10eeb2e7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:18:41 +0100
Subject: [PATCH 05/96] Add proper requirement for bam_to_bai converter

---
 lib/galaxy/datatypes/converters/bam_to_bai.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
index 1587ff83cab..094fb54948a 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -1,8 +1,8 @@
-<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" version="1.0.0" hidden="true">
+<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" version="1.0.0" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package">samtools</requirement>
+        <requirement type="package" version="1.10">samtools</requirement>
     </requirements>
-    <command>samtools index '$input1' '$output1'</command>
+    <command>samtools index -@ \${GALAXY_SLOTS:-1} '$input1' '$output1'</command>
     <inputs>
         <param format="bam" name="input1" type="data" label="Choose BAM"/>
     </inputs>

From d355b778c5fd3944b806d8855b7e77839d80604f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:19:18 +0100
Subject: [PATCH 06/96] Add python requirement to CONVERTER_bed_to_gff_0

---
 .../converters/bed_to_gff_converter.xml       |  5 +-
 tools/filters/bed_to_gff_converter.py         | 93 +++++++++----------
 2 files changed, 50 insertions(+), 48 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
index 26a4eeb2f2d..3d27e7408cf 100644
--- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
@@ -1,6 +1,9 @@
-<tool id="CONVERTER_bed_to_gff_0" name="Convert BED to GFF" version="2.0.0">
+<tool id="CONVERTER_bed_to_gff_0" name="Convert BED to GFF" version="2.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/bed_to_gff_converter.py' '$input1' '$output1'</command>
     <inputs>
         <param format="bed" name="input1" type="data" label="Choose BED file"/>
diff --git a/tools/filters/bed_to_gff_converter.py b/tools/filters/bed_to_gff_converter.py
index 768891fdcf8..fb7e0bd258f 100644
--- a/tools/filters/bed_to_gff_converter.py
+++ b/tools/filters/bed_to_gff_converter.py
@@ -12,60 +12,59 @@ def __main__():
     output_name = sys.argv[2]
     skipped_lines = 0
     first_skipped_line = 0
-    out = open(output_name, 'w')
     i = 0
-    for i, line in enumerate(open(input_name)):
-        complete_bed = False
-        line = line.rstrip('\r\n')
-        if line and not line.startswith('#') and not line.startswith('track') and not line.startswith('browser'):
-            try:
-                elems = line.split('\t')
-                if len(elems) == 12:
-                    complete_bed = True
-                chrom = elems[0]
-                if complete_bed:
-                    feature = "mRNA"
-                else:
+    with open(output_name, 'w') as out, open(input_name) as fh_in:
+        for i, line in enumerate(fh_in):
+            complete_bed = False
+            line = line.rstrip('\r\n')
+            if line and not line.startswith('#') and not line.startswith('track') and not line.startswith('browser'):
+                try:
+                    elems = line.split('\t')
+                    if len(elems) == 12:
+                        complete_bed = True
+                    chrom = elems[0]
+                    if complete_bed:
+                        feature = "mRNA"
+                    else:
+                        try:
+                            feature = elems[3]
+                        except Exception:
+                            feature = 'feature%d' % (i + 1)
+                    start = int(elems[1]) + 1
+                    end = int(elems[2])
                     try:
-                        feature = elems[3]
+                        score = elems[4]
                     except Exception:
-                        feature = 'feature%d' % (i + 1)
-                start = int(elems[1]) + 1
-                end = int(elems[2])
-                try:
-                    score = elems[4]
+                        score = '0'
+                    try:
+                        strand = elems[5]
+                    except Exception:
+                        strand = '+'
+                    try:
+                        group = elems[3]
+                    except Exception:
+                        group = 'group%d' % (i + 1)
+                    if complete_bed:
+                        out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
+                    else:
+                        out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n' % (chrom, feature, start, end, score, strand, group))
+                    if complete_bed:
+                        # We have all the info necessary to annotate exons for genes and mRNAs
+                        block_count = int(elems[9])
+                        block_sizes = elems[10].split(',')
+                        block_starts = elems[11].split(',')
+                        for j in range(block_count):
+                            exon_start = int(start) + int(block_starts[j])
+                            exon_end = exon_start + int(block_sizes[j]) - 1
+                            out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
                 except Exception:
-                    score = '0'
-                try:
-                    strand = elems[5]
-                except Exception:
-                    strand = '+'
-                try:
-                    group = elems[3]
-                except Exception:
-                    group = 'group%d' % (i + 1)
-                if complete_bed:
-                    out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
-                else:
-                    out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s;\n' % (chrom, feature, start, end, score, strand, group))
-                if complete_bed:
-                    # We have all the info necessary to annotate exons for genes and mRNAs
-                    block_count = int(elems[9])
-                    block_sizes = elems[10].split(',')
-                    block_starts = elems[11].split(',')
-                    for j in range(block_count):
-                        exon_start = int(start) + int(block_starts[j])
-                        exon_end = exon_start + int(block_sizes[j]) - 1
-                        out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
-            except Exception:
+                    skipped_lines += 1
+                    if not first_skipped_line:
+                        first_skipped_line = i + 1
+            else:
                 skipped_lines += 1
                 if not first_skipped_line:
                     first_skipped_line = i + 1
-        else:
-            skipped_lines += 1
-            if not first_skipped_line:
-                first_skipped_line = i + 1
-    out.close()
     info_msg = "%i lines converted to GFF version 2.  " % (i + 1 - skipped_lines)
     if skipped_lines > 0:
         info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)

From 5850751c3b7d1aa0826b74c38d563e0326bfeb56 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:19:43 +0100
Subject: [PATCH 07/96] Add pysam requirement to CONVERTER_bed_to_tabix_0

---
 lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
index 72c2b908de5..dd39eff96c5 100644
--- a/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_bed_to_tabix_0" name="Convert BED to tabix" version="1.0.0" hidden="true">
+<tool id="CONVERTER_bed_to_tabix_0" name="Convert BED to tabix" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_tabix_converter.py' -P bed '$input1' '$bgzip' '$output1'</command>
     <inputs>
         <param format="bed" name="input1" type="data" label="Choose BED file"/>

From b5beed012e4aa0c774b4c824f7d1b8d065b9c79e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:21:47 +0100
Subject: [PATCH 08/96] Add bx-python dependency for CONVERTER_BedGraph_0

---
 .../datatypes/converters/bedgraph_to_array_tree_converter.py | 3 +--
 .../converters/bedgraph_to_array_tree_converter.xml          | 5 ++++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
index 096b6a01254..a4f8b2d3a87 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
@@ -5,12 +5,11 @@ from __future__ import division
 import sys
 
 from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
-from six import Iterator
 
 BLOCK_SIZE = 100
 
 
-class BedGraphReader(Iterator):
+class BedGraphReader(object):
     def __init__(self, f):
         self.f = f
 
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
index f01a0408f02..1c7bda9754d 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_BedGraph_0" name="Index BedGraph for Track Viewer" version="1.0.0" hidden="true">
+<tool id="CONVERTER_BedGraph_0" name="Index BedGraph for Track Viewer" version="1.0.1" hidden="true" profile="16.04">
     <!-- Used internally to generate track indexes -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements
     <command>python '$__tool_directory__/bedgraph_to_array_tree_converter.py' '$input' '$output'</command>
     <inputs>
         <param format="bedgraph" name="input" type="data" label="Choose BedGraph"/>

From 155e288b2aa0b43975191273785885f86dc09ef7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:25:46 +0100
Subject: [PATCH 09/96] Add bx-python dependency on
 CONVERTER_bed_to_interval_index_0

---
 .../datatypes/converters/bed_to_interval_index_converter.xml | 5 ++++-
 .../converters/interval_to_interval_index_converter.py       | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
index bb171c0cd0b..ac35e961494 100644
--- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_bed_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true">
+<tool id="CONVERTER_bed_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_interval_index_converter.py' '$input1' '$output1'</command>
     <inputs>
         <param format="bed" name="input1" type="data" label="Choose BED file"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
index 54dbd2d16ed..29b727e5f53 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
@@ -44,7 +44,8 @@ def main():
         index.add(chrom, chrom_start, chrom_end, offset)
         offset += len(line)
 
-    index.write(open(output_fname, "w"))
+    with open(output_fname, 'w') as out:
+        index.write(out)
 
 
 if __name__ == "__main__":

From 3ddb0d2180d78d801e813da00793fca11d1a9440 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:27:59 +0100
Subject: [PATCH 10/96] Fix bedgraph_to_array_tree_converter.xml dependency

---
 .../converters/bedgraph_to_array_tree_converter.py | 14 ++++++++------
 .../bedgraph_to_array_tree_converter.xml           |  2 +-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
index a4f8b2d3a87..c2f90247eec 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
@@ -41,15 +41,17 @@ def main():
     input_fname = sys.argv[1]
     out_fname = sys.argv[2]
 
-    reader = BedGraphReader(open(input_fname))
+    with open(input_fname) as in_fh:
+        reader = BedGraphReader(in_fh)
 
-    # Fill array from reader
-    d = array_tree_dict_from_reader(reader, {}, block_size=BLOCK_SIZE)
+        # Fill array from reader
+        d = array_tree_dict_from_reader(reader, {}, block_size=BLOCK_SIZE)
 
-    for array_tree in d.values():
-        array_tree.root.build_summary()
+        for array_tree in d.values():
+            array_tree.root.build_summary()
 
-    FileArrayTreeDict.dict_to_file(d, open(out_fname, "w"))
+        with open(out_fname, 'w') as out:
+            FileArrayTreeDict.dict_to_file(d, out)
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
index 1c7bda9754d..4add42991c2 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
@@ -2,7 +2,7 @@
     <!-- Used internally to generate track indexes -->
     <requirements>
         <requirement type="package" version="0.8.6">bx-python</requirement>
-    </requirements
+    </requirements>
     <command>python '$__tool_directory__/bedgraph_to_array_tree_converter.py' '$input' '$output'</command>
     <inputs>
         <param format="bedgraph" name="input" type="data" label="Choose BedGraph"/>

From 468a8942f86c187dc38afbd9cf2ed8d9ac259988 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:29:46 +0100
Subject: [PATCH 11/96] Add bzip2 dependency for CONVERTER_bz2_to_uncompressed

---
 lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml b/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml
index 3d5ee318b78..ebe660218a0 100644
--- a/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml
+++ b/lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml
@@ -1,4 +1,7 @@
-<tool id="CONVERTER_bz2_to_uncompressed" name="Convert compressed file to uncompressed." version="1.0.0" hidden="true" profile="17.09">
+<tool id="CONVERTER_bz2_to_uncompressed" name="Convert compressed file to uncompressed." version="1.0.1" hidden="true" profile="17.09">
+  <requirements>
+    <requirement type="package" version="1.0.8">bzip2</requirement>
+  </requirements>
   <command><![CDATA[
     cp '$ext_config' 'galaxy.json' && bzip2 -dcf '$input1' > '$output1'
   ]]></command>

From d21c5866410468f53d3a15590fd1af0b6fcf9ed6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:32:22 +0100
Subject: [PATCH 12/96] Add pysam requirement to CONVERTER_cram_to_bam_0

---
 lib/galaxy/datatypes/converters/cram_to_bam_converter.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
index 440e72e4e81..a877bcd3320 100644
--- a/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
+++ b/lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
@@ -1,4 +1,7 @@
-<tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.0" hidden="true">
+<tool id="CONVERTER_cram_to_bam_0" name="Convert CRAM to BAM" version="1.0.0" hidden="true" profile="16.04">
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <command><![CDATA[python $__tool_directory__/cram_to_bam.py '$input' '$output']]></command>
     <inputs>
         <param format="cram" name="input" type="data" label="Choose CRAM file"/>

From 88e19590534388f6f325a1f73467e81ca4cc80ae Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:32:56 +0100
Subject: [PATCH 13/96] Add python requirement to csv_to_tabular

---
 lib/galaxy/datatypes/converters/csv_to_tabular.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/csv_to_tabular.xml b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
index 4a00b67e406..a90b70940b4 100644
--- a/lib/galaxy/datatypes/converters/csv_to_tabular.xml
+++ b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
@@ -1,5 +1,8 @@
-<tool id="csv_to_tabular" name="Convert CSV to tabular" version="1.0.0">
+<tool id="csv_to_tabular" name="Convert CSV to tabular" version="1.0.0" profile="16.04">
     <description></description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/tabular_csv.py' -o '$tabular' -i '$csv'</command>
     <inputs>
         <param format="csv" name="csv" type="data" label="Choose file with comma-separated values"/>

From 8bede93813c35e768dc20c5af98fef0d6dfad4cf Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:35:07 +0100
Subject: [PATCH 14/96] Add pysam requirement to interval_to_tabix_converter.py

---
 .../datatypes/converters/encodepeak_to_tabix_converter.xml   | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
index d3506653e84..8ba65850ba0 100644
--- a/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_encodepeak_to_tabix_0" name="Convert ENCODEPeak to tabix" version="1.0.0" hidden="true">
+<tool id="CONVERTER_encodepeak_to_tabix_0" name="Convert ENCODEPeak to tabix" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/interval_to_tabix_converter.py'
         -c ${input1.metadata.chromCol}

From 50c0965c9952c77484db2e4870a6752cb58331ef Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:40:04 +0100
Subject: [PATCH 15/96] Add python requirement to CONVERTER_fasta_to_len

---
 lib/galaxy/datatypes/converters/fasta_to_len.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.xml b/lib/galaxy/datatypes/converters/fasta_to_len.xml
index 74f021cd753..d86bf202f72 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.xml
@@ -1,6 +1,9 @@
-<tool id="CONVERTER_fasta_to_len" name="Convert FASTA to len file" version="1.0.0">
+<tool id="CONVERTER_fasta_to_len" name="Convert FASTA to len file" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/fasta_to_len.py' '$input' '$output' 0</command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>

From 480a34bc306d9c3797368eb6aab75132a8126e1b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:40:27 +0100
Subject: [PATCH 16/96] Add python requirement to CONVERTER_fasta_to_len

---
 .../datatypes/converters/fasta_to_tabular_converter.xml      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
index d87ae808905..8da4ffb00ac 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
@@ -1,6 +1,9 @@
-<tool id="CONVERTER_fasta_to_tabular" name="Convert FASTA to Tabular" version="1.0.1">
+<tool id="CONVERTER_fasta_to_tabular" name="Convert FASTA to Tabular" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/fasta_to_tabular_converter.py' '$input' '$output'</command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>

From 60a5c489242232e58d2db1365205c013d7a93679 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:40:54 +0100
Subject: [PATCH 17/96] Add python requirement to
 CONVERTER_fastqsolexa_to_fasta_0

---
 .../datatypes/converters/fastqsolexa_to_fasta_converter.py   | 3 +--
 .../datatypes/converters/fastqsolexa_to_fasta_converter.xml  | 5 ++++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
index 8ddb749ec91..86b0cd9a1cc 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
@@ -19,8 +19,7 @@ assert sys.version_info[:2] >= (2, 4)
 
 
 def stop_err(msg):
-    sys.stderr.write("%s" % msg)
-    sys.exit()
+    sys.exit("%s" % msg)
 
 
 def __main__():
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
index b4b1c89b00c..20b70bde298 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_fastqsolexa_to_fasta_0" name="Convert Fastqsolexa to Fasta" version="1.0.0">
+<tool id="CONVERTER_fastqsolexa_to_fasta_0" name="Convert Fastqsolexa to Fasta" version="1.0.0" profile="16.04">
     <description>converts Fastqsolexa file to Fasta format</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/fastqsolexa_to_fasta_converter.py' '$input' '$output'</command>
     <inputs>
         <param name="input" type="data" format="fastqsolexa" label="Choose Fastqsolexa file"/>

From 671fd7f130e360d42f318bf8998893eebb64d163 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:41:52 +0100
Subject: [PATCH 18/96] Add python requirement to
 CONVERTER_fastqsolexa_to_qual_0

---
 .../datatypes/converters/fastqsolexa_to_qual_converter.py    | 3 +--
 .../datatypes/converters/fastqsolexa_to_qual_converter.xml   | 5 ++++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
index e0aba894622..90fc5527ca7 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
@@ -19,8 +19,7 @@ assert sys.version_info[:2] >= (2, 4)
 
 
 def stop_err(msg):
-    sys.stderr.write("%s" % msg)
-    sys.exit()
+    sys.exit("%s" % msg)
 
 
 def __main__():
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
index b5ac900ae5e..8984e77ee29 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
@@ -1,4 +1,7 @@
-<tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual" version="1.0.0">
+<tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual" version="1.0.1" profile="16.04">
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/fastqsolexa_to_qual_converter.py' '$input1' '$output1' ${input1.extension}</command>
     <inputs>
         <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/>

From 69642bffad3097257805ff9a620284a972e1bdad Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:44:24 +0100
Subject: [PATCH 19/96] Use context manager in CONVERTER_gff_to_bed_0

---
 .../converters/gff_to_bed_converter.xml       |   2 +-
 tools/filters/gff_to_bed_converter.py         | 103 +++++++++---------
 2 files changed, 52 insertions(+), 53 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml b/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
index 4835288abe9..53f5ba14370 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_gff_to_bed_0" name="Convert GFF to BED" version="1.0.0">
+<tool id="CONVERTER_gff_to_bed_0" name="Convert GFF to BED" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <command>python '$__tool_directory__/gff_to_bed_converter.py' '$input1' '$output1'</command>
diff --git a/tools/filters/gff_to_bed_converter.py b/tools/filters/gff_to_bed_converter.py
index 1326188dd9b..929347ce959 100644
--- a/tools/filters/gff_to_bed_converter.py
+++ b/tools/filters/gff_to_bed_converter.py
@@ -55,29 +55,50 @@ def __main__():
     output_name = sys.argv[2]
     skipped_lines = 0
     first_skipped_line = 0
-    out = open(output_name, 'w')
     i = 0
     cur_transcript_chrome = None
     cur_transcript_id = None
     cur_transcript_strand = None
     cur_transcripts_blocks = []  # (start, end) for each block.
-    for i, line in enumerate(open(input_name)):
-        line = line.rstrip('\r\n')
-        if line and not line.startswith('#'):
-            try:
-                # GFF format: chrom source, name, chromStart, chromEnd, score, strand, attributes
-                elems = line.split('\t')
-                start = str(int(elems[3]) - 1)
-                coords = [int(start), int(elems[4])]
-                strand = elems[6]
-                if strand not in ['+', '-']:
-                    strand = '+'
-                attributes = parse_gff_attributes(elems[8])
-                t_id = attributes.get("transcript_id", None)
+    with open(output_name, 'w') as out, open(input_name) as in_fh:
+        for i, line in enumerate(in_fh):
+            line = line.rstrip('\r\n')
+            if line and not line.startswith('#'):
+                try:
+                    # GFF format: chrom source, name, chromStart, chromEnd, score, strand, attributes
+                    elems = line.split('\t')
+                    start = str(int(elems[3]) - 1)
+                    coords = [int(start), int(elems[4])]
+                    strand = elems[6]
+                    if strand not in ['+', '-']:
+                        strand = '+'
+                    attributes = parse_gff_attributes(elems[8])
+                    t_id = attributes.get("transcript_id", None)
+
+                    if not t_id:
+                        #
+                        # No transcript ID, so write last transcript and write current line as its own line.
+                        #
+
+                        # Write previous transcript.
+                        if cur_transcript_id:
+                            # Write BED entry.
+                            out.write(get_bed_line(cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks))
+
+                        # Replace any spaces in the name with underscores so UCSC will not complain.
+                        name = elems[2].replace(" ", "_")
+                        out.write(get_bed_line(elems[0], name, strand, [coords]))
+                        continue
+
+                    # There is a transcript ID, so process line at transcript level.
+                    if t_id == cur_transcript_id:
+                        # Line is element of transcript and will be a block in the BED entry.
+                        cur_transcripts_blocks.append(coords)
+                        continue
 
-                if not t_id:
                     #
-                    # No transcript ID, so write last transcript and write current line as its own line.
+                    # Line is part of new transcript; write previous transcript and start
+                    # new transcript.
                     #
 
                     # Write previous transcript.
@@ -85,47 +106,25 @@ def __main__():
                         # Write BED entry.
                         out.write(get_bed_line(cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks))
 
-                    # Replace any spaces in the name with underscores so UCSC will not complain.
-                    name = elems[2].replace(" ", "_")
-                    out.write(get_bed_line(elems[0], name, strand, [coords]))
-                    continue
-
-                # There is a transcript ID, so process line at transcript level.
-                if t_id == cur_transcript_id:
-                    # Line is element of transcript and will be a block in the BED entry.
+                    # Start new transcript.
+                    cur_transcript_chrome = elems[0]
+                    cur_transcript_id = t_id
+                    cur_transcript_strand = strand
+                    cur_transcripts_blocks = []
                     cur_transcripts_blocks.append(coords)
-                    continue
-
-                #
-                # Line is part of new transcript; write previous transcript and start
-                # new transcript.
-                #
-
-                # Write previous transcript.
-                if cur_transcript_id:
-                    # Write BED entry.
-                    out.write(get_bed_line(cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks))
-
-                # Start new transcript.
-                cur_transcript_chrome = elems[0]
-                cur_transcript_id = t_id
-                cur_transcript_strand = strand
-                cur_transcripts_blocks = []
-                cur_transcripts_blocks.append(coords)
-            except Exception:
+                except Exception:
+                    skipped_lines += 1
+                    if not first_skipped_line:
+                        first_skipped_line = i + 1
+            else:
                 skipped_lines += 1
                 if not first_skipped_line:
                     first_skipped_line = i + 1
-        else:
-            skipped_lines += 1
-            if not first_skipped_line:
-                first_skipped_line = i + 1
 
-    # Write last transcript.
-    if cur_transcript_id:
-        # Write BED entry.
-        out.write(get_bed_line(cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks))
-    out.close()
+        # Write last transcript.
+        if cur_transcript_id:
+            # Write BED entry.
+            out.write(get_bed_line(cur_transcript_chrome, cur_transcript_id, cur_transcript_strand, cur_transcripts_blocks))
     info_msg = "%i lines converted to BED.  " % (i + 1 - skipped_lines)
     if skipped_lines > 0:
         info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % (skipped_lines, first_skipped_line)

From 83c21c29b04a41e2164d5bddddbf0c0c54d70a69 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:47:35 +0100
Subject: [PATCH 20/96] Add profile version

---
 lib/galaxy/datatypes/converters/gff_to_fli_converter.xml        | 2 +-
 .../datatypes/converters/gff_to_interval_index_converter.xml    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
index 0cd2b0e46ed..200e7476786 100644
--- a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_gff_to_fli_0" name="Convert GFF to Feature Location Index" version="1.0.0">
+<tool id="CONVERTER_gff_to_fli_0" name="Convert GFF to Feature Location Index" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <command>python '$__tool_directory__/interval_to_fli.py' -F $input1.extension '$input1' '$output1'</command>
diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
index f5971eb197a..21292491c6f 100644
--- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_gff_to_interval_index_0" name="Convert GFF to Interval Index" version="1.0.0" hidden="true">
+<tool id="CONVERTER_gff_to_interval_index_0" name="Convert GFF to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <command>python '$__tool_directory__/gff_to_interval_index_converter.py' '$input1' '$output1'</command>
     <inputs>

From ebfc0c4639cdb8716671e22685117907c38c4956 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:48:38 +0100
Subject: [PATCH 21/96] Add pysam requirement for CONVERTER_gff_to_tabix_0

---
 lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml   | 5 ++++-
 .../datatypes/converters/interval_to_tabix_converter.py      | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
index ad0a6059970..fad1ea75a53 100644
--- a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_gff_to_tabix_0" name="Convert GFF to tabix" version="1.0.0" hidden="true">
+<tool id="CONVERTER_gff_to_tabix_0" name="Convert GFF to tabix" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_tabix_converter.py' -P gff '$input1' '$bgzip' '$output1'</command>
     <inputs>
         <param format="gff" name="input1" type="data" label="Choose GFF file"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
index faf988da48e..a4fec2bef4d 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
@@ -42,7 +42,7 @@ def to_tabix(bgzip_fname, out_fname, preset=None, chrom_col=None, start_col=None
                                         start_col=(start_col - 1), end_col=(end_col - 1),
                                         keep_original=True, index=out_fname, force=True)
     if os.path.getsize(out_fname) == 0:
-        sys.stderr.write("The converted tabix index file is empty, meaning the input data is invalid.")
+        sys.exit("The converted tabix index file is empty, meaning the input data is invalid.")
     return bgzip_fname
 
 

From 2eb459b9e5c02378f129336a2749cfba94887a66 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:50:38 +0100
Subject: [PATCH 22/96] Add bx-python dependency for
 CONVERTER_interval_to_bed12_0

---
 .../datatypes/converters/interval_to_bed12_converter.xml     | 5 ++++-
 .../datatypes/converters/interval_to_bedstrict_converter.py  | 3 +--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index 26bc669653a..c51db731e1b 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_interval_to_bed12_0" name="Convert Genomic Intervals To Strict BED12" version="1.0.0">
+<tool id="CONVERTER_interval_to_bed12_0" name="Convert Genomic Intervals To Strict BED12" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/interval_to_bedstrict_converter.py'
         '$output1' '$input1' ${input1.metadata.chromCol}
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
index 7a6dc10358f..e309292db44 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
@@ -10,8 +10,7 @@ assert sys.version_info[:2] >= (2, 6)
 
 
 def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(msg)
 
 
 def force_bed_field_count(fields, region_count, force_num_columns):

From 27ae74002897a1e2d94219b19855a8e625e3b048 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:51:35 +0100
Subject: [PATCH 23/96] Add bx-python dependency for
 CONVERTER_interval_to_bed6_0

---
 .../datatypes/converters/interval_to_bed6_converter.xml      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index 3130f5d8865..fefef47d81c 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_interval_to_bed6_0" name="Convert Genomic Intervals To Strict BED6" version="1.0.0">
+<tool id="CONVERTER_interval_to_bed6_0" name="Convert Genomic Intervals To Strict BED6" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
     <inputs>
         <param format="interval" name="input1" type="data" label="Choose intervals"/>

From 173bc9ef68b35d3c39fb83a7d50b9fbbc7b6fd28 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:52:35 +0100
Subject: [PATCH 24/96] Add bx-python dependency for
 CONVERTER_interval_to_bedstrict_0

---
 .../datatypes/converters/interval_to_bedstrict_converter.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index 47b3a7a4e4d..136a150413b 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_interval_to_bedstrict_0" name="Convert Genomic Intervals To Strict BED" version="1.0.0">
+<tool id="CONVERTER_interval_to_bedstrict_0" name="Convert Genomic Intervals To Strict BED" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
     <inputs>
         <param format="interval" name="input1" type="data" label="Choose intervals"/>

From e9fa45efce8939b9f287b153ce2fd42aa9686d61 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:53:35 +0100
Subject: [PATCH 25/96] Add bx-python dependency for
 CONVERTER_interval_to_coverage_0

---
 lib/galaxy/datatypes/converters/interval_to_coverage.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.xml b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
index 1b3a139fec9..1141f739ce7 100644
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_interval_to_coverage_0" name="Convert Genomic Intervals To COVERAGE" version="1.0.0">
+<tool id="CONVERTER_interval_to_coverage_0" name="Convert Genomic Intervals To COVERAGE" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/interval_to_coverage.py' '$input1' '$output1'
         -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}

From 85f1b546140a4d8fd4c8aad17ce6f533db9ba67f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:54:36 +0100
Subject: [PATCH 26/96] Add bx-python dependency for
 CONVERTER_interval_to_interval_index_0

---
 .../converters/interval_to_interval_index_converter.xml      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
index 67a480fe4e7..6ed6492c5bc 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_interval_to_interval_index_0" name="Convert Interval to Interval Index" version="1.0.0" hidden="true">
+<tool id="CONVERTER_interval_to_interval_index_0" name="Convert Interval to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/interval_to_interval_index_converter.py'
         -c ${input1.metadata.chromCol}

From 76ba57ee6a6fbd3c7b4372e0d93fe3b5862f9299 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:55:45 +0100
Subject: [PATCH 27/96] Add pysam dependency for CONVERTER_interval_to_tabix_0

---
 .../datatypes/converters/interval_to_tabix_converter.xml     | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
index 1e5d9974524..00373cd59dd 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
@@ -1,4 +1,7 @@
-<tool id="CONVERTER_interval_to_tabix_0" name="Convert Interval to tabix" version="1.0.0" hidden="true">
+<tool id="CONVERTER_interval_to_tabix_0" name="Convert Interval to tabix" version="1.0.1" hidden="true" profile="16.04">
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <command>
         python '$__tool_directory__/interval_to_tabix_converter.py'

From ac8c0ecfc1c369437de8d7d5eee109367a9bce72 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 15:57:20 +0100
Subject: [PATCH 28/96] Add pysam dependency for CONVERTER_len_to_linecount

---
 lib/galaxy/datatypes/converters/len_to_linecount.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/len_to_linecount.xml b/lib/galaxy/datatypes/converters/len_to_linecount.xml
index 9f638bfbda7..71ba698323e 100644
--- a/lib/galaxy/datatypes/converters/len_to_linecount.xml
+++ b/lib/galaxy/datatypes/converters/len_to_linecount.xml
@@ -1,6 +1,9 @@
-<tool id="CONVERTER_len_to_linecount" name="Convert Len file to Linecount" version="1.0.0">
+<tool id="CONVERTER_len_to_linecount" name="Convert Len file to Linecount" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="5.0.1">gawk</requirement>
+    </requirements>
     <command>
 <![CDATA[
         wc -l '$input' | awk '{print $1}' > '$output'

From 310878cdf92790db83e8bc217f8a74f1a3c429ed Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:03:56 +0100
Subject: [PATCH 29/96] Add python requirement for lped2fpedconvert

---
 .../datatypes/converters/lped_to_fped_converter.py       | 9 +++------
 .../datatypes/converters/lped_to_fped_converter.xml      | 5 ++++-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
index 2bc185310bf..81be44df3c5 100644
--- a/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
+++ b/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
@@ -42,13 +42,11 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
     try:
         mf = open(inmap, 'r')
     except Exception:
-        sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
-        sys.exit(1)
+        sys.exit('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
     try:
         rsl = [x.split()[1] for x in mf]
     except Exception:
-        sys.stderr.write('## cannot parse %s' % inmap)
-        sys.exit(1)
+        sys.exit('## cannot parse %s' % inmap)
     try:
         os.makedirs(outfilepath)
     except Exception:
@@ -85,8 +83,7 @@ def main():
     """
     nparm = 3
     if len(sys.argv) < nparm:
-        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
-        sys.exit(1)
+        sys.exit('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
     outfilepath = sys.argv[3]
diff --git a/lib/galaxy/datatypes/converters/lped_to_fped_converter.xml b/lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
index 16d0cab9686..da15908c80a 100644
--- a/lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
+++ b/lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
@@ -1,6 +1,9 @@
-<tool id="lped2fpedconvert" name="Convert lped to fped" version="0.01">
+<tool id="lped2fpedconvert" name="Convert lped to fped" version="0.02" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/lped_to_fped_converter.py' '$input1.extra_files_path/$input1.metadata.base_name' '$output1' '$output1.files_path'
     </command>

From d362b1ec51f1b9f41ec338bd8f83bac3750d4df1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:05:01 +0100
Subject: [PATCH 30/96] Add python requirement for lped2pbedconvert

---
 lib/galaxy/datatypes/converters/lped_to_pbed_converter.py  | 3 +--
 lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml | 5 ++++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
index 68fc19bc9c3..4201bc8fe22 100644
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
@@ -87,8 +87,7 @@ def main():
     """
     nparm = 4
     if len(sys.argv) < nparm:
-        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
-        sys.exit(1)
+        sys.exit('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
     outfilepath = sys.argv[3]
diff --git a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
index 40001ae9af8..fe434710368 100644
--- a/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
+++ b/lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
@@ -1,6 +1,9 @@
-<tool id="lped2pbedconvert" name="Convert lped to plink pbed" version="0.01">
+<tool id="lped2pbedconvert" name="Convert lped to plink pbed" version="0.02" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/lped_to_pbed_converter.py' '$input1.extra_files_path/$input1.metadata.base_name'
         '$output1' '$output1.files_path' 'plink'

From 7e7dfce8f69de7b4799a0101f07d2ff1e35bb823 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:07:11 +0100
Subject: [PATCH 31/96] Add profile to CONVERTER_maf_to_fasta_0

---
 lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
index 725d9789a47..51c2420bc38 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_maf_to_fasta_0" name="Convert MAF to Fasta" version="1.0.1">
+<tool id="CONVERTER_maf_to_fasta_0" name="Convert MAF to Fasta" version="1.0.2" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <command>python '$__tool_directory__/maf_to_fasta_converter.py' '$output1' '$input1'</command>
     <inputs>

From d56ad8ebd44fa40c8acf9593a2f901113427596d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:07:54 +0100
Subject: [PATCH 32/96] Add profile to CONVERTER_maf_to_interval_0

---
 lib/galaxy/datatypes/converters/maf_to_interval_converter.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
index fc2a04b06f7..6c3b3ef8d0e 100644
--- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
+++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
@@ -1,4 +1,4 @@
-<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.2">
+<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.3" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <command>python '$__tool_directory__/maf_to_interval_converter.py' '$output1' '$input1' '${input1.metadata.dbkey}'</command>
     <inputs>

From 6798edee09157d0772f9056b67d2ee719e01abb2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:09:28 +0100
Subject: [PATCH 33/96] Add unzip dependency for
 CONVERTER_neostorezip_to_neostore

---
 .../converters/neostorezip_to_neostore_converter.xml         | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml b/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
index 74486fe30d4..3ae5c09c564 100644
--- a/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
+++ b/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
@@ -1,4 +1,7 @@
-<tool id="CONVERTER_neostorezip_to_neostore" name="Convert neostore.zip files to neostore" version="1.0.0" hidden="true">
+<tool id="CONVERTER_neostorezip_to_neostore" name="Convert neostore.zip files to neostore" version="1.0.0" hidden="true" profile="16.04">
+  <requirements>
+    <requirement type="package" version="6.0">unzip</requirement>
+  </requirements>
   <command><![CDATA[
         unzip '${input1.extra_files_path}/neostore_file.zip' -d '${output1.files_path}' > $output1
         ]]>

From 9c314991011a9d3e2e1ca04ebebe80a3af617a71 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:10:44 +0100
Subject: [PATCH 34/96] Add python dependency for pbed2ldindepconvert

---
 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
index dfe22d6ae12..c48372b818f 100644
--- a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
+++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
@@ -1,5 +1,8 @@
-<tool id="pbed2ldindepconvert" name="Convert plink pbed to ld reduced format" version="0.01">
+<tool id="pbed2ldindepconvert" name="Convert plink pbed to ld reduced format" version="0.02" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/pbed_ldreduced_converter.py' '$input1.extra_files_path/$input1.metadata.base_name' '60' '55' '0.1' '$output1' '$output1.files_path' 'plink'
     </command>

From 2cf0d1e4837ca9931a2ad5e61417897c1dfedd60 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:11:47 +0100
Subject: [PATCH 35/96] Add python dependency for pbed2lpedconvert

---
 lib/galaxy/datatypes/converters/pbed_to_lped_converter.py  | 3 +--
 lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml | 5 ++++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
index e61aba09556..f7ed7689c80 100644
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
@@ -53,8 +53,7 @@ def main():
     """
     nparm = 4
     if len(sys.argv) < nparm:
-        sys.stderr.write('PBED to LPED converter called with %s - needs %d parameters \n' % (sys.argv, nparm))
-        sys.exit(1)
+        sys.exit('PBED to LPED converter called with %s - needs %d parameters \n' % (sys.argv, nparm))
     inpedfilepath = sys.argv[1]
     outhtmlname = sys.argv[2]
     outfilepath = sys.argv[3]
diff --git a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
index 0b19e2f20e3..0a308fd9b04 100644
--- a/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
+++ b/lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
@@ -1,6 +1,9 @@
-<tool id="pbed2lpedconvert" name="Convert plink pbed to linkage lped" version="0.01">
+<tool id="pbed2lpedconvert" name="Convert plink pbed to linkage lped" version="0.02" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/pbed_to_lped_converter.py' '$input1.extra_files_path/$input1.metadata.base_name'
         '$output1' '$output1.files_path' plink

From c46167edd474f744cb45191d02f772a68eab4e9a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:13:14 +0100
Subject: [PATCH 36/96] Add python dependency for
 CONVERTER_picard_interval_list_to_bed6

---
 .../converters/picard_interval_list_to_bed6_converter.xml    | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
index 99d31e7eb98..4f573473314 100644
--- a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_picard_interval_list_to_bed6" name="Convert Picard Interval List to BED6" version="1.0.0">
+<tool id="CONVERTER_picard_interval_list_to_bed6" name="Convert Picard Interval List to BED6" version="1.0.1" profile="16.04">
     <description>converter</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/picard_interval_list_to_bed6_converter.py' '$input' '$output'</command>
     <inputs>
         <param name="input" type="data" format="picard_interval_list" label="Picard Interval List file"/>

From cf7a02fbe2a6d99f0f6acab811066b0095a67c9c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:14:45 +0100
Subject: [PATCH 37/96] Add bx-python dependency for
 CONVERTER_pileup_to_interval_index_0

---
 .../converters/pileup_to_interval_index_converter.py         | 3 ++-
 .../converters/pileup_to_interval_index_converter.xml        | 5 ++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
index 02d781e1742..3fb7f1f4ccf 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
@@ -29,7 +29,8 @@ def main():
         index.add(chrom, start, start + 1, offset)
         offset += len(line)
 
-    index.write(open(output_fname, "w"))
+    with open(output_fname, 'w') as out:
+        index.write(out)
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
index a500ed866ff..e41f57b64fc 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.0" hidden="true">
+<tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>
         python '$__tool_directory__/pileup_to_interval_index_converter.py'
         '$input' '$output'

From 1fc1907373eec1f1ed67ed972d8a3b9dcec1adc7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:16:06 +0100
Subject: [PATCH 38/96] Add python dependency for CONVERTER_ref_to_seq_taxomony

---
 .../datatypes/converters/ref_to_seq_taxonomy_converter.xml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
index 2d1d9db87ed..6f0d114422f 100644
--- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
+++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_ref_to_seq_taxomony" name="Convert Ref taxonomy to Seq Taxonomy" version="1.0.0">
+<tool id="CONVERTER_ref_to_seq_taxomony" name="Convert Ref taxonomy to Seq Taxonomy" version="1.0.1" profile="16.04">
   <description>converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format</description>
+  <requirements>
+    <requirement type="package" version="3.7">python</requirement>
+  </requirements>
   <command> python '$__tool_directory__/ref_to_seq_taxonomy_converter.py' '$input' '$output'</command>
   <inputs>
     <param name="input" type="data" format="mothur.ref.taxonomy" label="a Sequence Taxomony file"/>
@@ -9,4 +12,4 @@
   </outputs>
   <help>
   </help>
-</tool>
\ No newline at end of file
+</tool>

From 84b818631e179a9e412ec7dde44734fa94e777f0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:18:51 +0100
Subject: [PATCH 39/96] Add python dependency for tabular_to_csv

---
 lib/galaxy/datatypes/converters/tabular_to_csv.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/tabular_to_csv.xml b/lib/galaxy/datatypes/converters/tabular_to_csv.xml
index 2c853109184..fadc2def328 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_csv.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_csv.xml
@@ -1,5 +1,8 @@
-<tool id="tabular_to_csv" name="Convert tabular to CSV" version="1.0.0">
+<tool id="tabular_to_csv" name="Convert tabular to CSV" version="1.0.0" profile="16.04">
     <description></description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/tabular_csv.py' --from-tabular -i '$tabular' -o '$csv'</command>
     <inputs>
         <param format="tsv,tabular" name="tabular" type="data" label="Choose file with tab-separated values"/>

From 2265d4a6548464c1f874ee0fd4309243e6dc275d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:20:42 +0100
Subject: [PATCH 40/96] Add python dependency for tabular_to_dbnsfp

---
 lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
index d82911bc912..2122229e3d1 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
@@ -1,5 +1,8 @@
-<tool id="tabular_to_dbnsfp" name="Convert tabular to dbnsfp" version="1.0.0">
+<tool id="tabular_to_dbnsfp" name="Convert tabular to dbnsfp" version="1.0.1" profile="16.04">
     <description></description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/tabular_to_dbnsfp.py' '$input' '$dbnsfp.extra_files_path/dbNSFP.gz'</command>
     <inputs>
         <param format="tabular" name="input" type="data" label="Choose a dbnsfp tabular file"/>

From 6e875ee38e5b314110764632d0de19f7007427f7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:21:01 +0100
Subject: [PATCH 41/96] Add pysam dependency for CONVERTER_vcf_bgzip_to_tabix_0

---
 .../datatypes/converters/vcf_bgzip_to_tabix_converter.xml    | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
index 64deb6df678..499e4c02402 100644
--- a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_vcf_bgzip_to_tabix_0" name="Convert BGZ VCF to tabix" version="1.0.0" hidden="true">
+<tool id="CONVERTER_vcf_bgzip_to_tabix_0" name="Convert BGZ VCF to tabix" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_tabix_converter.py' -P 'vcf' '' '$input1' '$output1'</command>
     <inputs>
         <param format="vcf_bgzip" name="input1" type="data" label="Choose BGZIP'd VCF file"/>

From 64a43aad693ac314c042dd6be8b07499d1e4cdf9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:23:56 +0100
Subject: [PATCH 42/96] Add bx-python, galaxy-sequence-utils  dependencies for
 CONVERTER_vcf_to_interval_index_0

---
 .../converters/vcf_to_interval_index_converter.xml          | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
index 03bf17d9709..d324832b4bd 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
@@ -1,5 +1,9 @@
-<tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.0" hidden="true">
+<tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description>
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="1.1.4">galaxy_sequence_utils</requirement>
+    </requirements>
     <command>python '$__tool_directory__/vcf_to_interval_index_converter.py' '$input1' '$output1'</command>
     <inputs>
         <param format="vcf" name="input1" type="data" label="Choose VCF file"/>

From 3cea1542f04139c06807e3a6cbf6be7e65865081 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:25:03 +0100
Subject: [PATCH 43/96] Add pysam  dependency for CONVERTER_vcf_to_tabix_0

---
 lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
index 41394394572..99954904d84 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_vcf_to_tabix_0" name="Convert Vcf to tabix" version="1.0.0" hidden="true">
+<tool id="CONVERTER_vcf_to_tabix_0" name="Convert Vcf to tabix" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+    <requirements>
+        <requirement type="package" version="0.15.4">pysam</requirement>
+    </requirements>
     <command>python '$__tool_directory__/interval_to_tabix_converter.py' -P vcf '$input1' '$bgzip' '$output1'</command>
     <inputs>
         <param format="vcf" name="input1" type="data" label="Choose Vcf file"/>

From f3ef378d182d363e85df166087e44ef326f1e287 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 16:29:32 +0100
Subject: [PATCH 44/96] Add bx-python dependency for CONVERTER_Wiggle_0

---
 .../converters/wiggle_to_array_tree_converter.py    | 13 +++++++------
 .../converters/wiggle_to_array_tree_converter.xml   |  5 ++++-
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
index 6dc81144ea6..12ed7a14af1 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
@@ -15,15 +15,16 @@ def main():
     input_fname = sys.argv[1]
     out_fname = sys.argv[2]
 
-    reader = WiggleReader(open(input_fname))
+    with input(input_fname) as in_fh, open(out_fname, 'w') as out:
+        reader = WiggleReader(in_fh)
 
-    # Fill array from reader
-    d = array_tree_dict_from_reader(reader, {}, block_size=BLOCK_SIZE)
+        # Fill array from reader
+        d = array_tree_dict_from_reader(reader, {}, block_size=BLOCK_SIZE)
 
-    for array_tree in d.values():
-        array_tree.root.build_summary()
+        for array_tree in d.values():
+            array_tree.root.build_summary()
 
-    FileArrayTreeDict.dict_to_file(d, open(out_fname, "w"))
+        FileArrayTreeDict.dict_to_file(d, out)
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
index 5ae0d98fd08..f15b12e7b33 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_Wiggle_0" name="Index Wiggle for Track Viewer" version="1.0.0" hidden="true">
+<tool id="CONVERTER_Wiggle_0" name="Index Wiggle for Track Viewer" version="1.0.1" hidden="true" profile="16.04">
     <!-- Used internally to generate track indexes -->
+    <requirements>
+        <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/wiggle_to_array_tree_converter.py' '$input' '$output'</command>
     <inputs>
         <param format="wiggle" name="input" type="data" label="Choose wiggle"/>

From 724a0b6b6a8ccaff16435c0e1122a890482675a4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 19:18:07 +0100
Subject: [PATCH 45/96] Add (automatically generated) tests for converters for
 which we have input data

---
 lib/galaxy/datatypes/converters/bam_to_bai.xml              | 6 ++++++
 lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml | 6 ++++++
 .../converters/bcf_to_bcf_uncompressed_converter.xml        | 6 ++++++
 .../converters/bed_gff_or_vcf_to_bigwig_converter.xml       | 6 ++++++
 lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml  | 6 ++++++
 lib/galaxy/datatypes/converters/bed_to_fli_converter.xml    | 6 ++++++
 lib/galaxy/datatypes/converters/bed_to_gff_converter.xml    | 6 ++++++
 .../converters/bed_to_interval_index_converter.xml          | 6 ++++++
 lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml  | 6 ++++++
 .../converters/bedgraph_to_array_tree_converter.xml         | 6 ++++++
 .../datatypes/converters/bedgraph_to_bigwig_converter.xml   | 6 ++++++
 lib/galaxy/datatypes/converters/biom1_to_biom2.xml          | 6 ++++++
 lib/galaxy/datatypes/converters/csv_to_tabular.xml          | 6 ++++++
 lib/galaxy/datatypes/converters/fasta_to_2bit.xml           | 6 ++++++
 .../converters/fasta_to_bowtie_base_index_converter.xml     | 6 ++++++
 .../converters/fasta_to_bowtie_color_index_converter.xml    | 6 ++++++
 lib/galaxy/datatypes/converters/fasta_to_fai.xml            | 6 ++++++
 lib/galaxy/datatypes/converters/fasta_to_len.xml            | 6 ++++++
 .../datatypes/converters/fasta_to_tabular_converter.xml     | 6 ++++++
 lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml          | 6 ++++++
 .../datatypes/converters/fastqsolexa_to_fasta_converter.xml | 6 ++++++
 .../datatypes/converters/fastqsolexa_to_qual_converter.xml  | 6 ++++++
 lib/galaxy/datatypes/converters/gff_to_bed_converter.xml    | 6 ++++++
 lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml  | 6 ++++++
 lib/galaxy/datatypes/converters/gff_to_fli_converter.xml    | 6 ++++++
 .../converters/gff_to_interval_index_converter.xml          | 6 ++++++
 lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml  | 6 ++++++
 .../datatypes/converters/interval_to_bed12_converter.xml    | 6 ++++++
 .../datatypes/converters/interval_to_bed6_converter.xml     | 6 ++++++
 .../datatypes/converters/interval_to_bed_converter.xml      | 6 ++++++
 .../converters/interval_to_bedstrict_converter.xml          | 6 ++++++
 .../datatypes/converters/interval_to_bgzip_converter.xml    | 6 ++++++
 .../datatypes/converters/interval_to_bigwig_converter.xml   | 6 ++++++
 lib/galaxy/datatypes/converters/interval_to_coverage.xml    | 6 ++++++
 .../converters/interval_to_interval_index_converter.xml     | 6 ++++++
 .../datatypes/converters/interval_to_tabix_converter.xml    | 6 ++++++
 lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml  | 6 ++++++
 .../datatypes/converters/maf_to_interval_converter.xml      | 6 ++++++
 .../converters/pileup_to_interval_index_converter.xml       | 6 ++++++
 lib/galaxy/datatypes/converters/sam_to_bam.xml              | 6 ++++++
 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml | 6 ++++++
 lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml     | 6 ++++++
 lib/galaxy/datatypes/converters/tabular_to_csv.xml          | 6 ++++++
 lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml       | 6 ++++++
 lib/galaxy/datatypes/converters/tar_to_directory.xml        | 6 ++++++
 .../datatypes/converters/to_coordinate_sorted_bam.xml       | 6 ++++++
 lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml     | 6 ++++++
 lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml  | 6 ++++++
 .../converters/vcf_to_interval_index_converter.xml          | 6 ++++++
 lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml  | 6 ++++++
 .../datatypes/converters/vcf_to_vcf_bgzip_converter.xml     | 6 ++++++
 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml | 6 ++++++
 .../datatypes/converters/wiggle_to_simple_converter.xml     | 6 ++++++
 53 files changed, 318 insertions(+)

diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
index 094fb54948a..65ace10fc93 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bai.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -9,6 +9,12 @@
     <outputs>
         <data format="bai" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bam" value="srma_out2.bam"/>
+            <output name="output1" format="bai" value="srma_out2.bai"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 7f8d8bcfeb3..0c13ca4f288 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -21,6 +21,12 @@ bedtools genomecov -bg -split -ibam '$input'
     <outputs>
         <data name="output" format="bigwig"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="bam" value="srma_out2.bam"/>
+            <output name="output" format="bigwig" value="srma_out2.bigwig"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml b/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
index 83bf34f11f7..39cf8b68860 100644
--- a/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
+++ b/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
@@ -12,6 +12,12 @@ bcftools view -o '$output1' -O u '$input1'
     <outputs>
         <data name="output1" format="bcf_uncompressed" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bcf" value="bcf_index_metadata_test.bcf"/>
+            <output name="output1" format="bcf_uncompressed" value="bcf_uncompressed_index_metadata_test.bcf_uncompressed"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
index cd64113d236..b79460164e0 100644
--- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -38,6 +38,12 @@
     <outputs>
         <data format="bigwig" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="bed" value="droPer1.bed"/>
+            <output name="output" format="bigwig" value="droPer1.bigwig"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
index c19d371f019..270b98bcf16 100644
--- a/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="bgzip" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bed" value="droPer1.bed"/>
+            <output name="output1" format="bgzip" value="droPer1.bgzip"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml b/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
index 2c3c55541ac..eb7ac28ea03 100644
--- a/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
@@ -8,6 +8,12 @@
     <outputs>
         <data format="fli" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bed" value="droPer1.bed"/>
+            <output name="output1" format="fli" value="droPer1.fli"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
index 3d27e7408cf..79ed48a9ef6 100644
--- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="gff" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bed" value="droPer1.bed"/>
+            <output name="output1" format="gff" value="droPer1.gff"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
index ac35e961494..8f8f9eda906 100644
--- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="interval_index" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bed" value="droPer1.bed"/>
+            <output name="output1" format="interval_index" value="droPer1.interval_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
index dd39eff96c5..cfedf148a3b 100644
--- a/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="tabix" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bed" value="droPer1.bed"/>
+            <output name="output1" format="tabix" value="droPer1.tabix"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
index 4add42991c2..013ee18e468 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="array_tree" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="bedgraph" value="gtf2bedgraph_out.bedgraph"/>
+            <output name="output" format="array_tree" value="gtf2array_tree_out.array_tree"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
index f842d0201f5..6015d94da4e 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="bigwig" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="bedgraph" value="gtf2bedgraph_out.bedgraph"/>
+            <output name="output" format="bigwig" value="gtf2bigwig_out.bigwig"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/biom1_to_biom2.xml b/lib/galaxy/datatypes/converters/biom1_to_biom2.xml
index 8dc76d09e26..33e2dc872d4 100644
--- a/lib/galaxy/datatypes/converters/biom1_to_biom2.xml
+++ b/lib/galaxy/datatypes/converters/biom1_to_biom2.xml
@@ -9,6 +9,12 @@
     <outputs>
         <data name="output" format="biom2"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="biom1" value="input_taxonomy.biom1"/>
+            <output name="output" format="biom2" value="input_taxonomy.biom2"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/csv_to_tabular.xml b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
index a90b70940b4..12129ee074f 100644
--- a/lib/galaxy/datatypes/converters/csv_to_tabular.xml
+++ b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="tabular" name="tabular"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="csv" format="csv" value="1.csv"/>
+            <output name="tabular" format="tabular" value="1.tabular"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
index 419e04c2ec8..65706581c4b 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data name="output" format="twobit"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fasta" value="chr_m.fasta"/>
+            <output name="output" format="twobit" value="chr_m.twobit"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
index 8b191f1376e..7482cd03c28 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
@@ -18,6 +18,12 @@
     <outputs>
         <data name="output" format="bowtie_base_index"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fasta" value="chr_m.fasta"/>
+            <output name="output" format="bowtie_base_index" value="chr_m.bowtie_base_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
index 81ebd75a23a..d72edeae150 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
@@ -19,6 +19,12 @@
     <outputs>
         <data name="output" format="bowtie_color_index"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fasta" value="chr_m.fasta"/>
+            <output name="output" format="bowtie_color_index" value="chr_m.bowtie_color_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_fai.xml b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
index b8d1d3b5b46..6d572fdde85 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_fai.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_fai.xml
@@ -12,6 +12,12 @@ samtools faidx temp.fasta
     <outputs>
         <data name="output" format="fai" from_work_dir="temp.fasta.fai" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fasta" value="chr_m.fasta"/>
+            <output name="output" format="fai" value="chr_m.fai"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.xml b/lib/galaxy/datatypes/converters/fasta_to_len.xml
index d86bf202f72..03dd3672463 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data name="output" format="len"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fasta" value="chr_m.fasta"/>
+            <output name="output" format="len" value="chr_m.len"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
index 8da4ffb00ac..f9722c7d493 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data name="output" format="tabular"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fasta" value="chr_m.fasta"/>
+            <output name="output" format="tabular" value="chr_m.tabular"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
index d8bb8ad377f..bd19fc6d117 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
@@ -6,6 +6,12 @@
     <outputs>
         <data format="fqtoc" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="fastq" value="shrimp_wrapper_test1.fastq"/>
+            <output name="output1" format="fqtoc" value="shrimp_wrapper_test1.fqtoc"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
index 20b70bde298..bba40736105 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data name="output" format="fasta"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="fastqsolexa" value="2.fastqsolexa"/>
+            <output name="output" format="fasta" value="2.fasta"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
index 8984e77ee29..eb0757db83b 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
@@ -9,6 +9,12 @@
     <outputs>
         <data format="qualsolexa" name="output1" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="fastqsolexa" value="2.fastqsolexa"/>
+            <output name="output1" format="qualsolexa" value="2.qualsolexa"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml b/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
index 53f5ba14370..1208586b05d 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
@@ -8,6 +8,12 @@
     <outputs>
         <data format="bed" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="gff" value="gff_filter_by_feature_count_out2.gff"/>
+            <output name="output1" format="bed" value="bed_filter_by_feature_count_out2.bed"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
index 412a6553caa..3dcfa1d18bd 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="bgzip" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="gff" value="gff_filter_by_feature_count_out2.gff"/>
+            <output name="output1" format="bgzip" value="bgzip_filter_by_feature_count_out2.bgzip"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
index 200e7476786..cba80687cf1 100644
--- a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
@@ -8,6 +8,12 @@
     <outputs>
         <data format="fli" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="gff" value="gff_filter_by_feature_count_out2.gff"/>
+            <output name="output1" format="fli" value="fli_filter_by_feature_count_out2.fli"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
index 21292491c6f..47a6e72d269 100644
--- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
@@ -7,6 +7,12 @@
     <outputs>
         <data format="interval_index" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="gff" value="gff_filter_by_feature_count_out2.gff"/>
+            <output name="output1" format="interval_index" value="interval_index_filter_by_feature_count_out2.interval_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
index fad1ea75a53..bb5fbbe1345 100644
--- a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="tabix" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="gff" value="gff_filter_by_feature_count_out2.gff"/>
+            <output name="output1" format="tabix" value="tabix_filter_by_feature_count_out2.tabix"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index c51db731e1b..29db5ce3169 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -16,6 +16,12 @@
     <outputs>
         <data format="bed12" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="bed12" value="2.bed12"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index fefef47d81c..bac6e58da86 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="bed6" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="bed6" value="2.bed6"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
index 11109b7d3e3..3eddcf5f8d8 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="bed" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="bed" value="2.bed"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index 136a150413b..ef1bdc26b8c 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="bedstrict" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="bedstrict" value="2.bedstrict"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index b630dac23d0..020f539d501 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -17,6 +17,12 @@
     <outputs>
         <data format="bgzip" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="bgzip" value="2.bgzip"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index 05654055e55..637e0ab6173 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -29,6 +29,12 @@
     <outputs>
         <data format="bigwig" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output" format="bigwig" value="2.bigwig"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.xml b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
index 1141f739ce7..9166f885054 100644
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
@@ -14,6 +14,12 @@
     <outputs>
         <data format="coverage" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="coverage" value="2.coverage"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
index 6ed6492c5bc..5cde6aeb1a4 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
@@ -16,6 +16,12 @@
     <outputs>
         <data format="interval_index" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="interval_index" value="2.interval_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
index 00373cd59dd..d99ee11d89b 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
@@ -17,6 +17,12 @@
     <outputs>
         <data format="tabix" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="interval" value="2.interval"/>
+            <output name="output1" format="tabix" value="2.tabix"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
index 51c2420bc38..824d8fc0f95 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
@@ -7,6 +7,12 @@
     <outputs>
         <data format="fasta" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="maf" value="interval2maf_3from28way.maf"/>
+            <output name="output1" format="fasta" value="interval2fasta_3from28way.fasta"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
index 6c3b3ef8d0e..6405dfb097d 100644
--- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
+++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
@@ -7,6 +7,12 @@
     <outputs>
         <data format="interval" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="maf" value="interval2maf_3from28way.maf"/>
+            <output name="output1" format="interval" value="interval2interval_3from28way.interval"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
index e41f57b64fc..66030851b71 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
@@ -13,6 +13,12 @@
     <outputs>
         <data format="interval_index" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="pileup" value="1.pileup"/>
+            <output name="output" format="interval_index" value="1.interval_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.xml b/lib/galaxy/datatypes/converters/sam_to_bam.xml
index 9a32a1d988e..f77feec0663 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bam.xml
@@ -15,6 +15,12 @@
     <outputs>
         <data name="output" format="bam"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="sam" value="bfast_out1.sam"/>
+            <output name="output" format="bam" value="bfast_out1.bam"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index 434c44b6a12..56ad7d6c61a 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -20,6 +20,12 @@ samtools view -bh '$input' | bedtools genomecov -bg -split -ibam stdin
     <outputs>
         <data name="output" format="bigwig"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="sam" value="bfast_out1.sam"/>
+            <output name="output" format="bigwig" value="bfast_out1.bigwig"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
index 2a99a793d27..46fa4af4ae7 100644
--- a/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
@@ -17,6 +17,12 @@
     <outputs>
         <data name="output" format="unsorted.bam"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="sam" value="bfast_out1.sam"/>
+            <output name="output" format="unsorted.bam" value="bfast_out1.unsorted.bam"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/tabular_to_csv.xml b/lib/galaxy/datatypes/converters/tabular_to_csv.xml
index fadc2def328..c449bc3614e 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_csv.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_csv.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="csv" name="csv"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="tabular" format="tabular" value="gtf_filter_by_attribute_values_list_in3.tabular"/>
+            <output name="csv" format="csv" value="gtf_filter_by_attribute_values_list_in3.csv"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
index 2122229e3d1..5d61c6119a4 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="snpsiftdbnsfp" name="dbnsfp"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="tabular" value="gtf_filter_by_attribute_values_list_in3.tabular"/>
+            <output name="dbnsfp" format="snpsiftdbnsfp" value="gtf_filter_by_attribute_values_list_in3.snpsiftdbnsfp"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/tar_to_directory.xml b/lib/galaxy/datatypes/converters/tar_to_directory.xml
index 6865b86ee1d..e2fd0f5d1f3 100644
--- a/lib/galaxy/datatypes/converters/tar_to_directory.xml
+++ b/lib/galaxy/datatypes/converters/tar_to_directory.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="directory" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="tar" value="unsafe.tar"/>
+            <output name="output1" format="directory" value="unsafe.directory"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
index 1e2889a921c..f47ee1efbff 100644
--- a/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
@@ -17,6 +17,12 @@
     <outputs>
         <data format="bam" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="sam" value="bfast_out1.sam"/>
+            <output name="output" format="bam" value="bfast_out1.bam"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
index ced46c0cc31..c2a4d8c53b7 100644
--- a/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
+++ b/lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
@@ -18,6 +18,12 @@
     <outputs>
         <data format="qname_sorted.bam" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="sam" value="bfast_out1.sam"/>
+            <output name="output" format="qname_sorted.bam" value="bfast_out1.qname_sorted.bam"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
index 7986ce2efe6..be9d42400c3 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="bgzip" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="vcf" value="vcf_to_maf_in.vcf"/>
+            <output name="output1" format="bgzip" value="bgzip_to_maf_in.bgzip"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
index d324832b4bd..b74f0cd844a 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="interval_index" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="vcf" value="vcf_to_maf_in.vcf"/>
+            <output name="output1" format="interval_index" value="interval_index_to_maf_in.interval_index"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
index 99954904d84..984695d4b39 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="tabix" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="vcf" value="vcf_to_maf_in.vcf"/>
+            <output name="output1" format="tabix" value="tabix_to_maf_in.tabix"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
index daa84accc25..4a78f175c11 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
@@ -11,6 +11,12 @@
     <outputs>
         <data format="vcf_bgzip" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="vcf" value="vcf_to_maf_in.vcf"/>
+            <output name="output1" format="vcf_bgzip" value="vcf_bgzip_to_maf_in.vcf_bgzip"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index 862016e9151..281f68ecf14 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -15,6 +15,12 @@
     <outputs>
         <data format="bigwig" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="wig" value="aggregate_binned_scores_3.wig"/>
+            <output name="output" format="bigwig" value="aggregate_binned_scores_3.bigwig"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
index 29c494189ad..0273777e20f 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
@@ -8,4 +8,10 @@
     <outputs>
         <data format="interval" name="out_file1" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="wig" value="aggregate_binned_scores_3.wig"/>
+            <output name="out_file1" format="interval" value="aggregate_binned_scores_3.interval"/>
+        </test>
+    </tests>
 </tool>

From 70e01ff286de0072b7722dfe888523bf77d5d3fb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 09:22:58 +0100
Subject: [PATCH 46/96] Need to specify a dbkey

---
 .../datatypes/converters/bam_to_bigwig_converter.xml       | 7 ++++---
 lib/galaxy/datatypes/converters/dbkeys.loc.test            | 2 ++
 lib/galaxy/datatypes/converters/hg17.len                   | 1 +
 .../datatypes/converters/tool_data_table_conf.xml.test     | 7 +++++++
 4 files changed, 14 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy/datatypes/converters/dbkeys.loc.test
 create mode 100644 lib/galaxy/datatypes/converters/hg17.len
 create mode 100644 lib/galaxy/datatypes/converters/tool_data_table_conf.xml.test

diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
index 0c13ca4f288..53abc0a9c5c 100644
--- a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,8 +1,9 @@
 <tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.2" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.27.1">bedtools</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.29.2">bedtools</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 bedtools genomecov -bg -split -ibam '$input'
@@ -23,7 +24,7 @@ bedtools genomecov -bg -split -ibam '$input'
     </outputs>
     <tests>
         <test>
-            <param name="input" format="bam" value="srma_out2.bam"/>
+            <param name="input" format="bam" value="srma_out2.bam" dbkey="hg17"/>
             <output name="output" format="bigwig" value="srma_out2.bigwig"/>
         </test>
     </tests>
diff --git a/lib/galaxy/datatypes/converters/dbkeys.loc.test b/lib/galaxy/datatypes/converters/dbkeys.loc.test
new file mode 100644
index 00000000000..2c13efb0fc0
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/dbkeys.loc.test
@@ -0,0 +1,2 @@
+#<dbkey>	<display_name>	<len_file_path>
+hg17	hg17	${__HERE__}/hg17.len
diff --git a/lib/galaxy/datatypes/converters/hg17.len b/lib/galaxy/datatypes/converters/hg17.len
new file mode 100644
index 00000000000..b277a36162d
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/hg17.len
@@ -0,0 +1 @@
+dummy_chr	100000000
diff --git a/lib/galaxy/datatypes/converters/tool_data_table_conf.xml.test b/lib/galaxy/datatypes/converters/tool_data_table_conf.xml.test
new file mode 100644
index 00000000000..d88d1d880ef
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/tool_data_table_conf.xml.test
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of dbkeys and len files under genome directory -->
+    <table name="__dbkeys__" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, len_path</columns>
+        <file path="${__HERE__}/dbkeys.loc.test" />
+    </table>
+</tables>

From d8343c66984848e70844d84a87769aca5e3311ac Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 09:50:00 +0100
Subject: [PATCH 47/96] Add dbkey and chromosomes where necessary

---
 .../bed_gff_or_vcf_to_bigwig_converter.xml    |  2 +-
 .../bedgraph_to_bigwig_converter.xml          |  4 ++--
 .../fastqsolexa_to_fasta_converter.xml        |  2 +-
 lib/galaxy/datatypes/converters/hg17.len      | 23 +++++++++++++++++++
 .../interval_to_bigwig_converter.xml          |  2 +-
 .../converters/sam_to_bigwig_converter.xml    |  2 +-
 .../converters/wig_to_bigwig_converter.xml    |  2 +-
 7 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
index b79460164e0..2b2d7ab6f53 100644
--- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -40,7 +40,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" format="bed" value="droPer1.bed"/>
+            <param name="input" format="bed" value="droPer1.bed" dbkey="hg17"/>
             <output name="output" format="bigwig" value="droPer1.bigwig"/>
         </test>
     </tests>
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
index 6015d94da4e..b984cd3d43f 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -12,8 +12,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" format="bedgraph" value="gtf2bedgraph_out.bedgraph"/>
-            <output name="output" format="bigwig" value="gtf2bigwig_out.bigwig"/>
+            <param name="input" format="bedgraph" value="1.bedgraph" dbkey="hg17"/>
+            <output name="output" format="bigwig" value="1.bedgrpah_to_bigwig.bigwig"/>
         </test>
     </tests>
     <help>
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
index bba40736105..ff528b6f65f 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
@@ -13,7 +13,7 @@
     <tests>
         <test>
             <param name="input" format="fastqsolexa" value="2.fastqsolexa"/>
-            <output name="output" format="fasta" value="2.fasta"/>
+            <output name="output" format="fasta" value="2.fastqsolexa.fasta"/>
         </test>
     </tests>
     <help>
diff --git a/lib/galaxy/datatypes/converters/hg17.len b/lib/galaxy/datatypes/converters/hg17.len
index b277a36162d..dfd510997bb 100644
--- a/lib/galaxy/datatypes/converters/hg17.len
+++ b/lib/galaxy/datatypes/converters/hg17.len
@@ -1 +1,24 @@
 dummy_chr	100000000
+super_1	100000000
+chr1	100000000
+chr7	100000000
+chrX	100000000
+random_phiX_region_1	100000000
+random_phiX_region_2	100000000
+random_phiX_region_3	100000000
+random_phiX_region_4	100000000
+random_phiX_region_5	100000000
+random_phiX_region_6	100000000
+random_phiX_region_7	100000000
+random_phiX_region_8	100000000
+random_phiX_region_9	100000000
+random_phiX_region_10	100000000
+random_phiX_region_11	100000000
+random_phiX_region_12	100000000
+random_phiX_region_13	100000000
+random_phiX_region_14	100000000
+random_phiX_region_15	100000000
+random_phiX_region_16	100000000
+random_phiX_region_17	100000000
+random_phiX_region_18	100000000
+random_phiX_region_19	100000000
diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index 637e0ab6173..4e5e748f413 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -31,7 +31,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input1" format="interval" value="2.interval"/>
+            <param name="input1" format="interval" value="2.interval" dbkey="hg17"/>
             <output name="output" format="bigwig" value="2.bigwig"/>
         </test>
     </tests>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index 56ad7d6c61a..94ab9981480 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -22,7 +22,7 @@ samtools view -bh '$input' | bedtools genomecov -bg -split -ibam stdin
     </outputs>
     <tests>
         <test>
-            <param name="input" format="sam" value="bfast_out1.sam"/>
+            <param name="input" format="sam" value="bfast_out1.sam" dbkey="hg17"/>
             <output name="output" format="bigwig" value="bfast_out1.bigwig"/>
         </test>
     </tests>
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index 281f68ecf14..4666b41ed99 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -17,7 +17,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" format="wig" value="aggregate_binned_scores_3.wig"/>
+            <param name="input" format="wig" value="aggregate_binned_scores_3.wig" dbkey="hg17"/>
             <output name="output" format="bigwig" value="aggregate_binned_scores_3.bigwig"/>
         </test>
     </tests>

From 7eed087c304e000a7f5555799c3f2da32e4114bf Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 09:50:27 +0100
Subject: [PATCH 48/96] Avoid test data mixup

---
 lib/galaxy/datatypes/converters/interval_to_bed_converter.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
index 3eddcf5f8d8..2ae06465195 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
@@ -14,7 +14,7 @@
     <tests>
         <test>
             <param name="input1" format="interval" value="2.interval"/>
-            <output name="output1" format="bed" value="2.bed"/>
+            <output name="output1" format="bed" value="2.interval_to_bed.bed"/>
         </test>
     </tests>
     <help>

From 5b93fb5b312f0467aa29989496d4d019515907f6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 11:03:55 +0100
Subject: [PATCH 49/96] Compare uncompressed bcf by size

---
 .../datatypes/converters/bcf_to_bcf_uncompressed_converter.xml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml b/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
index 39cf8b68860..b3b79270ef6 100644
--- a/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
+++ b/lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
@@ -15,7 +15,7 @@ bcftools view -o '$output1' -O u '$input1'
     <tests>
         <test>
             <param name="input1" format="bcf" value="bcf_index_metadata_test.bcf"/>
-            <output name="output1" format="bcf_uncompressed" value="bcf_uncompressed_index_metadata_test.bcf_uncompressed"/>
+            <output name="output1" format="bcf_uncompressed" value="bcf_uncompressed_index_metadata_test.bcf_uncompressed" compare="sim_size"/>
         </test>
     </tests>
     <help>

From f15ebbbd1d20beb76235134d368534aa59e02bcc Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 11:04:14 +0100
Subject: [PATCH 50/96] Add missing chromosomes

---
 lib/galaxy/datatypes/converters/hg17.len | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/hg17.len b/lib/galaxy/datatypes/converters/hg17.len
index dfd510997bb..3206662bc66 100644
--- a/lib/galaxy/datatypes/converters/hg17.len
+++ b/lib/galaxy/datatypes/converters/hg17.len
@@ -1,8 +1,9 @@
 dummy_chr	100000000
 super_1	100000000
 chr1	100000000
-chr7	100000000
+chr7	200000000
 chrX	100000000
+phiX174	100000000
 random_phiX_region_1	100000000
 random_phiX_region_2	100000000
 random_phiX_region_3	100000000

From a5ee62dfb736ab1ebb7df2557e14d9df6ff8f79d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 12:27:52 +0100
Subject: [PATCH 51/96] Compare biom1_to_biom2  output by size

---
 lib/galaxy/datatypes/converters/biom1_to_biom2.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/biom1_to_biom2.xml b/lib/galaxy/datatypes/converters/biom1_to_biom2.xml
index 33e2dc872d4..672bba616ea 100644
--- a/lib/galaxy/datatypes/converters/biom1_to_biom2.xml
+++ b/lib/galaxy/datatypes/converters/biom1_to_biom2.xml
@@ -12,7 +12,7 @@
     <tests>
         <test>
             <param name="input" format="biom1" value="input_taxonomy.biom1"/>
-            <output name="output" format="biom2" value="input_taxonomy.biom2"/>
+            <output name="output" format="biom2" value="input_taxonomy.biom2" compare="sim_size"/>
         </test>
     </tests>
     <help>

From 641b295476f401dee2b7febcef004c676bad5f12 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 12:28:12 +0100
Subject: [PATCH 52/96] gff_to_interval_index_converter index is binary

---
 .../datatypes/converters/gff_to_interval_index_converter.py     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
index 6dda96b944f..2f5e131e2c9 100644
--- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
@@ -34,7 +34,7 @@ def main():
         # not included in the index.
         offset += feature.raw_size
 
-    index.write(open(out_fname, "w"))
+    index.write(open(out_fname, "wb"))
 
 
 if __name__ == "__main__":

From 680e11d719138c6b34207e073420499d810978a1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 12:28:54 +0100
Subject: [PATCH 53/96] Use python 3.6 for bx-python
 (https://github.com/bxlab/bx-python/pull/57)

---
 lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml  | 1 +
 lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml   | 1 +
 .../datatypes/converters/interval_to_bedstrict_converter.xml     | 1 +
 3 files changed, 3 insertions(+)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index 29db5ce3169..7507c53a231 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -2,6 +2,7 @@
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
         <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_bedstrict_converter.py'
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index bac6e58da86..2a966a2190a 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -2,6 +2,7 @@
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
         <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index ef1bdc26b8c..76685a8178e 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -2,6 +2,7 @@
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
         <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="3.6">python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
     <inputs>

From 5ea73caad8d0181afe7c14817b6f4f5af5a817ee Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Fri, 7 Feb 2020 18:34:12 -0500
Subject: [PATCH 54/96] Py2/3 compatibility for TSV/CSV conversion.

---
 lib/galaxy/datatypes/converters/tabular_csv.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/tabular_csv.py b/lib/galaxy/datatypes/converters/tabular_csv.py
index 0b18e1571e5..300140f2051 100644
--- a/lib/galaxy/datatypes/converters/tabular_csv.py
+++ b/lib/galaxy/datatypes/converters/tabular_csv.py
@@ -7,7 +7,17 @@ usage: %prog [--from-tabular] -i in_file -o out_file
 
 import argparse
 import csv
+import sys
 
+from contextlib import contextmanager
+
+@contextmanager
+def compat_open(file, mode):
+    if sys.version_info[0] > 2:
+        fh = open(file, mode, newline='')
+    else:
+        fh = open(file, mode + 'b')
+    yield fh
 
 def main():
     usage = "Usage: %prog [options]"
@@ -25,16 +35,16 @@ def main():
 
 
 def convert_to_tsv(input_fname, output_fname):
-    with open(input_fname, 'rb') as csvfile:
-        with open(output_fname, 'wb') as ofh:
+    with compat_open(input_fname, 'r') as csvfile:
+        with compat_open(output_fname, 'w') as ofh:
             reader = csv.reader(csvfile)
             for line in reader:
                 ofh.write('\t'.join(line) + '\n')
 
 
 def convert_to_csv(input_fname, output_fname):
-    with open(input_fname, 'rb') as tabfile:
-        with open(output_fname, 'wb') as ofh:
+    with compat_open(input_fname, 'r') as tabfile:
+        with compat_open(output_fname, 'w') as ofh:
             writer = csv.writer(ofh, delimiter=',')
             for line in tabfile.readlines():
                 writer.writerow(line.strip().split('\t'))

From adc511080f798f52a6fa19e618a650e3332729be Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 12:33:09 +0100
Subject: [PATCH 55/96] Drop python 2 compatibility

---
 .../datatypes/converters/tabular_csv.py       | 28 ++++++-------------
 1 file changed, 8 insertions(+), 20 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/tabular_csv.py b/lib/galaxy/datatypes/converters/tabular_csv.py
index 300140f2051..a323385037a 100644
--- a/lib/galaxy/datatypes/converters/tabular_csv.py
+++ b/lib/galaxy/datatypes/converters/tabular_csv.py
@@ -7,17 +7,7 @@ usage: %prog [--from-tabular] -i in_file -o out_file
 
 import argparse
 import csv
-import sys
 
-from contextlib import contextmanager
-
-@contextmanager
-def compat_open(file, mode):
-    if sys.version_info[0] > 2:
-        fh = open(file, mode, newline='')
-    else:
-        fh = open(file, mode + 'b')
-    yield fh
 
 def main():
     usage = "Usage: %prog [options]"
@@ -35,19 +25,17 @@ def main():
 
 
 def convert_to_tsv(input_fname, output_fname):
-    with compat_open(input_fname, 'r') as csvfile:
-        with compat_open(output_fname, 'w') as ofh:
-            reader = csv.reader(csvfile)
-            for line in reader:
-                ofh.write('\t'.join(line) + '\n')
+    with open(input_fname, newline="") as csvfile, open(output_fname, 'w') as ofh:
+        reader = csv.reader(csvfile)
+        for line in reader:
+            ofh.write('\t'.join(line) + '\n')
 
 
 def convert_to_csv(input_fname, output_fname):
-    with compat_open(input_fname, 'r') as tabfile:
-        with compat_open(output_fname, 'w') as ofh:
-            writer = csv.writer(ofh, delimiter=',')
-            for line in tabfile.readlines():
-                writer.writerow(line.strip().split('\t'))
+    with open(input_fname) as tabfile, open(output_fname, 'w', newline='') as ofh:
+        writer = csv.writer(ofh, delimiter=',')
+        for line in tabfile.readlines():
+            writer.writerow(line.strip().split('\t'))
 
 
 if __name__ == "__main__":

From 33e9053bebbbd7288436143325796e8df2ab74c6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 12:33:37 +0100
Subject: [PATCH 56/96] Fix tar_to_directory input

---
 lib/galaxy/datatypes/converters/tar_to_directory.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/tar_to_directory.xml b/lib/galaxy/datatypes/converters/tar_to_directory.xml
index e2fd0f5d1f3..0b8c18c1ded 100644
--- a/lib/galaxy/datatypes/converters/tar_to_directory.xml
+++ b/lib/galaxy/datatypes/converters/tar_to_directory.xml
@@ -13,8 +13,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="input1" format="tar" value="unsafe.tar"/>
-            <output name="output1" format="directory" value="unsafe.directory"/>
+            <param name="input1" format="tar" value="testdir1.tar"/>
+            <output name="output1" format="directory" value="testdir1.tar.directory"/>
         </test>
     </tests>
     <help>

From ab9df81ecbb6a3790b9f3fb2e22b207a57edc1f6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 13:08:02 +0100
Subject: [PATCH 57/96] Avoid test data conflict

---
 lib/galaxy/datatypes/converters/csv_to_tabular.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/csv_to_tabular.xml b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
index 12129ee074f..95809c39c80 100644
--- a/lib/galaxy/datatypes/converters/csv_to_tabular.xml
+++ b/lib/galaxy/datatypes/converters/csv_to_tabular.xml
@@ -13,7 +13,7 @@
     <tests>
         <test>
             <param name="csv" format="csv" value="1.csv"/>
-            <output name="tabular" format="tabular" value="1.tabular"/>
+            <output name="tabular" format="tabular" value="1.csv_to_tabular.tabular"/>
         </test>
     </tests>
     <help>

From 5e738cf7043701dabbb9926edc939a949cd8517d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 13:08:30 +0100
Subject: [PATCH 58/96] Bump up chrX size for interval_to_bigwig_converter test

---
 lib/galaxy/datatypes/converters/hg17.len | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/hg17.len b/lib/galaxy/datatypes/converters/hg17.len
index 3206662bc66..801131eeb22 100644
--- a/lib/galaxy/datatypes/converters/hg17.len
+++ b/lib/galaxy/datatypes/converters/hg17.len
@@ -2,7 +2,7 @@ dummy_chr	100000000
 super_1	100000000
 chr1	100000000
 chr7	200000000
-chrX	100000000
+chrX	200000000
 phiX174	100000000
 random_phiX_region_1	100000000
 random_phiX_region_2	100000000

From 235fe4df1106035d546c32380fe4e5dbab7a6438 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 13:09:11 +0100
Subject: [PATCH 59/96] Update interval_to_bigwig_converter dependencies,
 compare bigwig with sim_size

---
 .../datatypes/converters/interval_to_bigwig_converter.xml  | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index 4e5e748f413..684001e6a03 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -1,8 +1,9 @@
 <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.1">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package" version="2.27.1">bedtools</requirement>
+        <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.29.2">bedtools</requirement>
+        <requirement type="package" version="8.25">coreutils</requirement>
     </requirements>
     <command>
 <![CDATA[
@@ -32,7 +33,7 @@
     <tests>
         <test>
             <param name="input1" format="interval" value="2.interval" dbkey="hg17"/>
-            <output name="output" format="bigwig" value="2.bigwig"/>
+            <output name="output" format="bigwig" value="2.bigwig" compare="sim_size"/>
         </test>
     </tests>
     <help>

From 795c621b6ee1eb1f9a2712147493a65f1a423ccb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 14:53:48 +0100
Subject: [PATCH 60/96] Add more tests

---
 .../converters/bcf_uncompressed_to_bcf_converter.xml   |  6 ++++++
 lib/galaxy/datatypes/converters/biom2_to_biom1.xml     | 10 ++++++++++
 lib/galaxy/datatypes/converters/len_to_linecount.xml   |  6 ++++++
 .../converters/vcf_bgzip_to_tabix_converter.xml        |  6 ++++++
 4 files changed, 28 insertions(+)

diff --git a/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml b/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
index faf09918f64..a7f5b48813f 100644
--- a/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
+++ b/lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
@@ -12,6 +12,12 @@ bcftools view -o '$output1' -O b '$input1'
     <outputs>
         <data name="output1" format="bcf" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="bcf_uncompressed" value="bcf_uncompressed_index_metadata_test.bcf_uncompressed"/>
+            <output name="output1" format="bcf" value="bcf_index_metadata_test.bcf" compare="sim_size"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/biom2_to_biom1.xml b/lib/galaxy/datatypes/converters/biom2_to_biom1.xml
index 559763ff74f..a280bd84432 100644
--- a/lib/galaxy/datatypes/converters/biom2_to_biom1.xml
+++ b/lib/galaxy/datatypes/converters/biom2_to_biom1.xml
@@ -9,6 +9,16 @@
     <outputs>
         <data name="output" format="biom1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="biom2" value="input_taxonomy.biom2"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Biological Observation Matrix 1.0.0"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/len_to_linecount.xml b/lib/galaxy/datatypes/converters/len_to_linecount.xml
index 71ba698323e..db451e80bf8 100644
--- a/lib/galaxy/datatypes/converters/len_to_linecount.xml
+++ b/lib/galaxy/datatypes/converters/len_to_linecount.xml
@@ -15,6 +15,12 @@
     <outputs>
         <data name="output" format="linecount"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" format="len" value="chr_m.len"/>
+            <output name="output" format="linecount" value="chr_m.linecount"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>
diff --git a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
index 499e4c02402..da7188930c9 100644
--- a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
@@ -10,6 +10,12 @@
     <outputs>
         <data format="tabix" name="output1"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="input1" format="vcf_bgzip" value="vcf_bgzip_to_maf_in.vcf_bgzip"/>
+            <output name="output1" format="tabix" value="tabix_to_maf_in.tabix"/>
+        </test>
+    </tests>
     <help>
     </help>
 </tool>

From 4f491754eb5b97153c299ad74594f8738c0220c4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 10 Feb 2020 14:57:35 +0100
Subject: [PATCH 61/96] Avoid test-data conflict

---
 .../datatypes/converters/vcf_bgzip_to_tabix_converter.xml       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
index da7188930c9..cd5b477bc37 100644
--- a/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
@@ -13,7 +13,7 @@
     <tests>
         <test>
             <param name="input1" format="vcf_bgzip" value="vcf_bgzip_to_maf_in.vcf_bgzip"/>
-            <output name="output1" format="tabix" value="tabix_to_maf_in.tabix"/>
+            <output name="output1" format="tabix" value="tabix_to_maf_in_to_tabix.tabix"/>
         </test>
     </tests>
     <help>

From 2a66a39ace1afed85d449677402cec78850bd39b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 11:54:27 +0100
Subject: [PATCH 62/96] Add test that should provoke
 https://github.com/galaxyproject/galaxy/issues/9074

---
 test/unit/tools/test_tool_shed_repository_cache.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/test/unit/tools/test_tool_shed_repository_cache.py b/test/unit/tools/test_tool_shed_repository_cache.py
index 383d8351191..c14b2058f35 100644
--- a/test/unit/tools/test_tool_shed_repository_cache.py
+++ b/test/unit/tools/test_tool_shed_repository_cache.py
@@ -54,3 +54,13 @@ def test_get_installed_repository(tool_shed_repository_cache, repos, tool_conf_r
         assert repo
     else:
         assert repo is None
+
+
+def test_repo_cache_expunge(tool_shed_repository_cache, repos):
+    tool_shed_repository_cache.rebuild()
+    assert len(tool_shed_repository_cache.repositories) == 10
+    repo = tool_shed_repository_cache.repositories[0]
+    repo.name = 'new name'
+    tool_shed_repository_cache.app.install_model.session.flush()
+    tool_shed_repository_cache.app.install_model.session.remove()
+    assert repo.changeset_revision == "1"

From ff319b5fcdb503dc5404bc39baca782d78304055 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 11:54:56 +0100
Subject: [PATCH 63/96] Fix ParentInstanceDetached due to expire_on_commit

---
 lib/galaxy/tools/cache.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index 768d1b1ab07..e501bf3c84a 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -149,12 +149,22 @@ class ToolShedRepositoryCache(object):
         self.repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
 
     def rebuild(self):
-        self.repositories = self.app.install_model.context.current.query(self.app.install_model.ToolShedRepository).options(
+        session = self.app.install_model.context.current
+        self.repositories = session.query(self.app.install_model.ToolShedRepository).options(
             defer(self.app.install_model.ToolShedRepository.metadata),
             joinedload('tool_dependencies').subqueryload('tool_shed_repository').options(
                 defer(self.app.install_model.ToolShedRepository.metadata)
             ),
         ).all()
+        for r in self.repositories:
+            # We use sqlalchemy's expire_on_commit option for sessions,
+            # which means that attributes are fetched from the database
+            # after a commit occurs.
+            # The session used for establishing the cache however may have been closed,
+            # leading to ParentInstanceDetached errors.
+            # Expunging the repo prevents the refresh and should be
+            # safe since the cache will be rebuilt upon repository installations and uninstallations.
+            session.expunge(r)
         repos_by_tuple = defaultdict(list)
         for repository in self.repositories + self.local_repositories:
             repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)

From 098419b9b442c8556012d5cc68a2ad1d9657a5ff Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 12:21:39 +0100
Subject: [PATCH 64/96] Ensure repository metadata isn't kept in memory

---
 test/unit/tools/test_tool_shed_repository_cache.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/test/unit/tools/test_tool_shed_repository_cache.py b/test/unit/tools/test_tool_shed_repository_cache.py
index c14b2058f35..81da72c0a08 100644
--- a/test/unit/tools/test_tool_shed_repository_cache.py
+++ b/test/unit/tools/test_tool_shed_repository_cache.py
@@ -1,4 +1,5 @@
 import pytest
+from sqlalchemy.orm.exc import DetachedInstanceError
 
 from .conftest import create_repo
 
@@ -64,3 +65,7 @@ def test_repo_cache_expunge(tool_shed_repository_cache, repos):
     tool_shed_repository_cache.app.install_model.session.flush()
     tool_shed_repository_cache.app.install_model.session.remove()
     assert repo.changeset_revision == "1"
+    with pytest.raises(DetachedInstanceError):
+        # Make sure this still raises DetachedInstanceError,
+        # keeping this in memory would be expensive
+        repo.metadata

From 82a06af664aa14857f12bb866b075e4c2adf1a01 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 12:24:40 +0100
Subject: [PATCH 65/96] Explain why the test does what it does

---
 test/unit/tools/test_tool_shed_repository_cache.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/unit/tools/test_tool_shed_repository_cache.py b/test/unit/tools/test_tool_shed_repository_cache.py
index 81da72c0a08..f479d0d0f5f 100644
--- a/test/unit/tools/test_tool_shed_repository_cache.py
+++ b/test/unit/tools/test_tool_shed_repository_cache.py
@@ -60,9 +60,11 @@ def test_get_installed_repository(tool_shed_repository_cache, repos, tool_conf_r
 def test_repo_cache_expunge(tool_shed_repository_cache, repos):
     tool_shed_repository_cache.rebuild()
     assert len(tool_shed_repository_cache.repositories) == 10
+    # Modify and commit a repo, will expire in memory attributes of orm objects (unless expunged)
     repo = tool_shed_repository_cache.repositories[0]
     repo.name = 'new name'
     tool_shed_repository_cache.app.install_model.session.flush()
+    # remove session, so access to expired attributes will raise exception
     tool_shed_repository_cache.app.install_model.session.remove()
     assert repo.changeset_revision == "1"
     with pytest.raises(DetachedInstanceError):

From f4e32636e11f3b662ac5f260bd133926b9a34789 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 12:35:16 +0100
Subject: [PATCH 66/96] Make sure tool dependency relationships are accessibly
 as well

---
 test/unit/tools/conftest.py                        | 9 +++++++++
 test/unit/tools/test_tool_shed_repository_cache.py | 1 +
 2 files changed, 10 insertions(+)

diff --git a/test/unit/tools/conftest.py b/test/unit/tools/conftest.py
index a7de3f768bc..ab8d702131e 100644
--- a/test/unit/tools/conftest.py
+++ b/test/unit/tools/conftest.py
@@ -65,4 +65,13 @@ def create_repo(app, changeset, installed_changeset, config_filename=None):
     repository.deleted = False
     repository.uninstalled = False
     app.install_model.context.add(repository)
+    app.install_model.context.flush()
+    tool_dependency = tool_shed_install.ToolDependency(
+        name='Name',
+        version='100',
+        type='package',
+        status='ok',
+        tool_shed_repository_id=repository.id,
+    )
+    app.install_model.context.add(tool_dependency)
     return repository
diff --git a/test/unit/tools/test_tool_shed_repository_cache.py b/test/unit/tools/test_tool_shed_repository_cache.py
index f479d0d0f5f..a8db483deb8 100644
--- a/test/unit/tools/test_tool_shed_repository_cache.py
+++ b/test/unit/tools/test_tool_shed_repository_cache.py
@@ -67,6 +67,7 @@ def test_repo_cache_expunge(tool_shed_repository_cache, repos):
     # remove session, so access to expired attributes will raise exception
     tool_shed_repository_cache.app.install_model.session.remove()
     assert repo.changeset_revision == "1"
+    assert repo.tool_dependencies[0].name == 'Name'
     with pytest.raises(DetachedInstanceError):
         # Make sure this still raises DetachedInstanceError,
         # keeping this in memory would be expensive

From 8a8c0990dd1e79169377ca731ea4ac122c492b98 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 14:57:24 +0100
Subject: [PATCH 67/96] Give ToolShedRepositoryCache.rebuild its own session

---
 lib/galaxy/tools/cache.py                     | 34 ++++++++-----------
 .../tools/test_tool_shed_repository_cache.py  |  4 +--
 2 files changed, 16 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/tools/cache.py b/lib/galaxy/tools/cache.py
index e501bf3c84a..36ce418ab75 100644
--- a/lib/galaxy/tools/cache.py
+++ b/lib/galaxy/tools/cache.py
@@ -149,26 +149,20 @@ class ToolShedRepositoryCache(object):
         self.repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
 
     def rebuild(self):
-        session = self.app.install_model.context.current
-        self.repositories = session.query(self.app.install_model.ToolShedRepository).options(
-            defer(self.app.install_model.ToolShedRepository.metadata),
-            joinedload('tool_dependencies').subqueryload('tool_shed_repository').options(
-                defer(self.app.install_model.ToolShedRepository.metadata)
-            ),
-        ).all()
-        for r in self.repositories:
-            # We use sqlalchemy's expire_on_commit option for sessions,
-            # which means that attributes are fetched from the database
-            # after a commit occurs.
-            # The session used for establishing the cache however may have been closed,
-            # leading to ParentInstanceDetached errors.
-            # Expunging the repo prevents the refresh and should be
-            # safe since the cache will be rebuilt upon repository installations and uninstallations.
-            session.expunge(r)
-        repos_by_tuple = defaultdict(list)
-        for repository in self.repositories + self.local_repositories:
-            repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
-        self.repos_by_tuple = repos_by_tuple
+        try:
+            session = self.app.install_model.context.current.session_factory()
+            self.repositories = session.query(self.app.install_model.ToolShedRepository).options(
+                defer(self.app.install_model.ToolShedRepository.metadata),
+                joinedload('tool_dependencies').subqueryload('tool_shed_repository').options(
+                    defer(self.app.install_model.ToolShedRepository.metadata)
+                ),
+            ).all()
+            repos_by_tuple = defaultdict(list)
+            for repository in self.repositories + self.local_repositories:
+                repos_by_tuple[(repository.tool_shed, repository.owner, repository.name)].append(repository)
+            self.repos_by_tuple = repos_by_tuple
+        finally:
+            session.close()
 
     def get_installed_repository(self, tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None):
         if repository_id:
diff --git a/test/unit/tools/test_tool_shed_repository_cache.py b/test/unit/tools/test_tool_shed_repository_cache.py
index a8db483deb8..ae99298292e 100644
--- a/test/unit/tools/test_tool_shed_repository_cache.py
+++ b/test/unit/tools/test_tool_shed_repository_cache.py
@@ -60,11 +60,11 @@ def test_get_installed_repository(tool_shed_repository_cache, repos, tool_conf_r
 def test_repo_cache_expunge(tool_shed_repository_cache, repos):
     tool_shed_repository_cache.rebuild()
     assert len(tool_shed_repository_cache.repositories) == 10
-    # Modify and commit a repo, will expire in memory attributes of orm objects (unless expunged)
+    # Modify and commit a repo, will expire in memory attributes of orm objects (unless using a different session)
     repo = tool_shed_repository_cache.repositories[0]
     repo.name = 'new name'
     tool_shed_repository_cache.app.install_model.session.flush()
-    # remove session, so access to expired attributes will raise exception
+    # remove session, should demonstrate the separate session is in use
     tool_shed_repository_cache.app.install_model.session.remove()
     assert repo.changeset_revision == "1"
     assert repo.tool_dependencies[0].name == 'Name'

From eac0ff9d7f867b4bea10ed5772f8f1c789124b31 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 7 Feb 2020 09:49:26 +0100
Subject: [PATCH 68/96] Fix vcf_to_maf_customtrack

---
 lib/galaxy/tools/__init__.py         |  2 +-
 tools/maf/vcf_to_maf_customtrack.py  |  2 +-
 tools/maf/vcf_to_maf_customtrack.xml | 14 +++++++++-----
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index fdb9b1209d3..f3d65ba6e67 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -127,7 +127,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "send_to_cloud",
     "__DATA_FETCH__",
     # Legacy tools bundled with Galaxy.
-    "vcf_to_maf_customtrack1",
     "laj_1",
     "secure_hash_message_digest",
     "join1",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "PEsortedSAM2readprofile": packaging.version.parse("1.1.1"),
     "sam_to_bam": packaging.version.parse("1.1.3"),
     "sam_pileup": packaging.version.parse("1.1.3"),
+    "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
 }
 
 
diff --git a/tools/maf/vcf_to_maf_customtrack.py b/tools/maf/vcf_to_maf_customtrack.py
index 5c7a2bce376..73b7e2387b9 100644
--- a/tools/maf/vcf_to_maf_customtrack.py
+++ b/tools/maf/vcf_to_maf_customtrack.py
@@ -77,7 +77,7 @@ def main():
     if not (options.population ^ options.sample):
         parser.error('You must specify either a per population conversion or a per sample conversion, but not both')
 
-    out = open(args.pop(0), 'wb')
+    out = open(args.pop(0), 'w')
     out.write('track name="%s" visibility=pack\n' % options.name.replace("\"", "'"))
 
     maf_writer = bx.align.maf.Writer(out)
diff --git a/tools/maf/vcf_to_maf_customtrack.xml b/tools/maf/vcf_to_maf_customtrack.xml
index c10618ac41e..69f535755e0 100644
--- a/tools/maf/vcf_to_maf_customtrack.xml
+++ b/tools/maf/vcf_to_maf_customtrack.xml
@@ -1,5 +1,9 @@
-<tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track" version="1.0.0">
+<tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track" version="1.0.1">
   <description>for display at UCSC</description>
+  <requirements>
+    <requirement type="package" version="1.1.3">galaxy_sequence_utils</requirement>
+    <requirement type="package" version="0.8.6">bx-python</requirement>
+  </requirements>
   <macros>
       <import>macros.xml</import>
   </macros>
@@ -43,21 +47,21 @@ ${vcf_source_type.vcf_source} -n '$track_name'
   <outputs>
     <data format="mafcustomtrack" name="out_file1" />
   </outputs>
-<!--  <tests>
+  <tests>
     <test>
       <param name="track_name" value="Galaxy Custom Track"/>
-      <param name="vcf_source" value="Per Population"/>
+      <param name="vcf_source" value="-p"/>
       <param name="vcf_input" value="vcf_to_maf_in.vcf" ftype="tabular"/>
       <param name="population_name" value=""/>
       <output name="out_file1" file="vcf_to_maf_population_out.mafcustomtrack"/>
     </test>
     <test>
       <param name="track_name" value="Galaxy Custom Track"/>
-      <param name="vcf_source" value="Per Sample"/>
+      <param name="vcf_source" value="-s"/>
       <param name="vcf_input" value="vcf_to_maf_in.vcf" ftype="tabular"/>
       <output name="out_file1" file="vcf_to_maf_sample_out.mafcustomtrack"/>
     </test>
-  </tests> -->
+  </tests>
   <help>
 **What it does**
 

From af4fdf7e1f77a0e73ee81b67517b44db5c747e59 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 7 Feb 2020 18:06:42 +0100
Subject: [PATCH 69/96] Drop __next__

---
 tools/maf/vcf_to_maf_customtrack.py | 60 +++++++++++++----------------
 1 file changed, 26 insertions(+), 34 deletions(-)

diff --git a/tools/maf/vcf_to_maf_customtrack.py b/tools/maf/vcf_to_maf_customtrack.py
index 73b7e2387b9..5b89907c5e1 100644
--- a/tools/maf/vcf_to_maf_customtrack.py
+++ b/tools/maf/vcf_to_maf_customtrack.py
@@ -13,51 +13,43 @@ UNKNOWN_NUCLEOTIDE = '*'
 
 class PopulationVCFParser(Iterator):
     def __init__(self, reader, name):
-        self.reader = reader
+        self.reader = iter(reader)
         self.name = name
         self.counter = 0
 
-    def __next__(self):
-        rval = []
-        vc = next(self.reader)
-        for i, allele in enumerate(vc.alt):
-            rval.append(('%s_%i.%i' % (self.name, i + 1, self.counter + 1), allele))
-        self.counter += 1
-        return (vc, rval)
-
     def __iter__(self):
-        while True:
-            yield next(self)
+        for vc in self.reader:
+            rval = []
+            for i, allele in enumerate(vc.alt):
+                rval.append(('%s_%i.%i' % (self.name, i + 1, self.counter + 1), allele))
+            self.counter += 1
+            yield (vc, rval)
 
 
 class SampleVCFParser(Iterator):
     def __init__(self, reader):
-        self.reader = reader
+        self.reader = iter(reader)
         self.counter = 0
 
-    def __next__(self):
-        rval = []
-        vc = next(self.reader)
-        alleles = [vc.ref] + vc.alt
-
-        if 'GT' in vc.format:
-            gt_index = vc.format.index('GT')
-            for sample_name, sample_value in zip(vc.sample_names, vc.sample_values):
-                gt_indexes = []
-                for i in sample_value[gt_index].replace('|', '/').replace('\\', '/').split('/'):  # Do we need to consider phase here?
-                    try:
-                        gt_indexes.append(int(i))
-                    except Exception:
-                        gt_indexes.append(None)
-                for i, allele_i in enumerate(gt_indexes):
-                    if allele_i is not None:
-                        rval.append(('%s_%i.%i' % (sample_name, i + 1, self.counter + 1), alleles[allele_i]))
-        self.counter += 1
-        return (vc, rval)
-
     def __iter__(self):
-        while True:
-            yield next(self)
+        for vc in self.reader:
+            rval = []
+            alleles = [vc.ref] + vc.alt
+
+            if 'GT' in vc.format:
+                gt_index = vc.format.index('GT')
+                for sample_name, sample_value in zip(vc.sample_names, vc.sample_values):
+                    gt_indexes = []
+                    for i in sample_value[gt_index].replace('|', '/').replace('\\', '/').split('/'):  # Do we need to consider phase here?
+                        try:
+                            gt_indexes.append(int(i))
+                        except Exception:
+                            gt_indexes.append(None)
+                    for i, allele_i in enumerate(gt_indexes):
+                        if allele_i is not None:
+                            rval.append(('%s_%i.%i' % (sample_name, i + 1, self.counter + 1), alleles[allele_i]))
+            self.counter += 1
+            yield (vc, rval)
 
 
 def main():

From 7d166eb24d737fbce10747d3b7178e99c349cfee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 7 Feb 2020 18:06:55 +0100
Subject: [PATCH 70/96] Bump version and add profile

---
 tools/maf/vcf_to_maf_customtrack.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/maf/vcf_to_maf_customtrack.xml b/tools/maf/vcf_to_maf_customtrack.xml
index 69f535755e0..39b97ebe761 100644
--- a/tools/maf/vcf_to_maf_customtrack.xml
+++ b/tools/maf/vcf_to_maf_customtrack.xml
@@ -1,7 +1,7 @@
-<tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track" version="1.0.1">
+<tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track" version="1.0.1" profile="18.01">
   <description>for display at UCSC</description>
   <requirements>
-    <requirement type="package" version="1.1.3">galaxy_sequence_utils</requirement>
+    <requirement type="package" version="1.1.4">galaxy_sequence_utils</requirement>
     <requirement type="package" version="0.8.6">bx-python</requirement>
   </requirements>
   <macros>

From 1b7a36b2e4b19d8ff6af94a8d47852b8abff8fdd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 7 Feb 2020 18:52:50 +0100
Subject: [PATCH 71/96] Move secure_hash_message_digest to 
 GALAXY_LIB_TOOLS_VERSIONED

And give it its own dependency.
---
 lib/galaxy/tools/__init__.py                 | 2 +-
 tools/filters/secure_hash_message_digest.xml | 8 ++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index f3d65ba6e67..d9833cbcb59 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -128,7 +128,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "__DATA_FETCH__",
     # Legacy tools bundled with Galaxy.
     "laj_1",
-    "secure_hash_message_digest",
     "join1",
     "gff2bed1",
     "gff_filter_by_feature_count",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "sam_to_bam": packaging.version.parse("1.1.3"),
     "sam_pileup": packaging.version.parse("1.1.3"),
     "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
+    "secure_hash_message_digest": packaging.version.parse("0.0.2"),
 }
 
 
diff --git a/tools/filters/secure_hash_message_digest.xml b/tools/filters/secure_hash_message_digest.xml
index e20ce80969a..50554c7181d 100644
--- a/tools/filters/secure_hash_message_digest.xml
+++ b/tools/filters/secure_hash_message_digest.xml
@@ -1,6 +1,10 @@
-<tool id="secure_hash_message_digest" name="Secure Hash / Message Digest" version="0.0.1">
+<tool id="secure_hash_message_digest" name="Secure Hash / Message Digest" version="0.0.2" profile="18.01">
     <description>on a dataset</description>
-    <command interpreter="python">secure_hash_message_digest.py --input "${input1}" --output "${out_file1}"
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command>
+    python '$__tool_directory__/secure_hash_message_digest.py' --input '${input1}' --output '${out_file1}'
         #if $algorithms.value:
             #for $algorithm in str( $algorithms ).split( "," ):
                 --algorithm "${algorithm}"

From 25497155631a9e177d16ed199fa964f368cb2dee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 7 Feb 2020 19:48:50 +0100
Subject: [PATCH 72/96] Make join1 use proper requirements, move to
 GALAXY_LIB_TOOLS_VERSIONED

---
 lib/galaxy/tools/__init__.py |  2 +-
 tools/filters/joiner.xml     | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index d9833cbcb59..b25397258d5 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -128,7 +128,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "__DATA_FETCH__",
     # Legacy tools bundled with Galaxy.
     "laj_1",
-    "join1",
     "gff2bed1",
     "gff_filter_by_feature_count",
     "aggregate_scores_in_intervals2",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "sam_pileup": packaging.version.parse("1.1.3"),
     "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
     "secure_hash_message_digest": packaging.version.parse("0.0.2"),
+    "join1": packaging.version.parse("2.1.3"),
 }
 
 
diff --git a/tools/filters/joiner.xml b/tools/filters/joiner.xml
index 642d1e8b429..a1fc30f18bf 100644
--- a/tools/filters/joiner.xml
+++ b/tools/filters/joiner.xml
@@ -1,15 +1,15 @@
-<tool id="join1" name="Join two Datasets" version="2.1.2">
+<tool id="join1" name="Join two Datasets" version="2.1.3">
   <description>side by side on a specified field</description>
   <requirements>
-    <requirement type="package" version="2.7.13">python</requirement>
+    <requirement type="package" version="19.9.0">galaxy-util</requirement>
   </requirements>
   <command detect_errors="aggressive">
     python '$__tool_directory__/join.py' '$input1' '$input2' $field1 $field2 '$out_file1' $unmatched $partial --index_depth=3 --buffer=50000000 --fill_options_file=$fill_options_file $header
   </command>
   <configfiles>
-    <configfile name="fill_options_file">&lt;%
+    <configfile name="fill_options_file"><![CDATA[<%
 import json
-%&gt;
+%>
 #set $__fill_options = {}
 #if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
     #set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only'
@@ -30,7 +30,7 @@ import json
     #end if
 #end if
 ${json.dumps( __fill_options )}
-    </configfile>
+    ]]></configfile>
   </configfiles>
   <inputs>
     <param format="tabular" name="input1" type="data" label="Join"/>
@@ -174,7 +174,7 @@ ${json.dumps( __fill_options )}
       <output name="out_file1" file="joiner_out7.tab"/>
     </test>
   </tests>
-  <help>
+  <help><![CDATA
 
 .. class:: warningmark
 
@@ -182,7 +182,7 @@ ${json.dumps( __fill_options )}
 
 .. class:: infomark
 
-**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
 
 -----
 
@@ -221,6 +221,6 @@ Joining the 4th column of Dataset1 with the 1st column of Dataset2, while keepin
   chr1 50 80 geneB geneB Foxp2
   chr5 10 40 geneL
 
-</help>
+]]></help>
 <citations></citations>
 </tool>

From c05a9af4c87b60f2eec2b98a88fa7348babffa2b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 11:49:46 +0100
Subject: [PATCH 73/96] Move wiggle_to_interval out of
 GALAXY_LIB_TOOLS_UNVERSIONED

---
 .../converters/wiggle_to_simple_converter.py  | 34 ++++------------
 .../converters/wiggle_to_simple_converter.xml |  6 ++-
 lib/galaxy/tools/__init__.py                  |  4 +-
 tools/filters/wiggle_to_simple.py             | 40 +++++--------------
 tools/filters/wiggle_to_simple.xml            |  8 +++-
 5 files changed, 31 insertions(+), 61 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
index ac965e105ae..b2c3229bc86 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
@@ -11,40 +11,20 @@ import sys
 
 import bx.wiggle
 
-from galaxy.util import unicodify
 from galaxy.util.ucsc import (
     UCSCLimitException,
     UCSCOutWrapper
 )
 
 
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit(1)
-
-
 def main():
-    if len(sys.argv) > 1:
-        in_file = open(sys.argv[1])
-    else:
-        in_file = open(sys.stdin)
-
-    if len(sys.argv) > 2:
-        out_file = open(sys.argv[2], "w")
-    else:
-        out_file = sys.stdout
-
-    try:
-        for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-            out_file.write("%s\n" % "\t".join(map(str, fields)))
-    except UCSCLimitException:
-        # Wiggle data was truncated, at the very least need to warn the user.
-        print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
-    except ValueError as e:
-        stop_err(unicodify(e))
-    finally:
-        in_file.close()
-        out_file.close()
+    with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
+        try:
+            for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
+                out_file.write("%s\n" % "\t".join(map(str, fields)))
+        except UCSCLimitException:
+            # Wiggle data was truncated, at the very least need to warn the user.
+            sys.stderr.write('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
index 29c494189ad..5befe7746dc 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
@@ -1,6 +1,10 @@
-<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval" version="1.0.0">
+<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
+    <requirements>
+      <requirement type="package" version="19.09">galaxy-util</requirement>
+      <requirement type="package" version="0.8.6">bx-python</requirement>
+    </requirements>
     <command>python '$__tool_directory__/wiggle_to_simple_converter.py' '$input' '$out_file1'</command>
     <inputs>
         <param format="wig" name="input" type="data" label="Convert"/>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index b25397258d5..66a58102a1a 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -143,7 +143,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "MAF_split_blocks_by_species1",
     "MAF_Limit_To_Species1",
     "maf_by_block_number1",
-    "wiggle2simple1",
     # Converters
     "CONVERTER_bed_to_fli_0",
     "CONVERTER_fastq_to_fqtoc0",
@@ -151,7 +150,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",
     "CONVERTER_maf_to_interval_0",
-    "CONVERTER_wiggle_to_interval_0",
     "CONVERTER_tar_to_directory",
     # Tools improperly migrated to the tool shed (devteam)
     "qualityFilter",
@@ -191,6 +189,8 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "vcf_to_maf_customtrack1": packaging.version.parse("1.0.1"),
     "secure_hash_message_digest": packaging.version.parse("0.0.2"),
     "join1": packaging.version.parse("2.1.3"),
+    "wiggle2simple1": packaging.version.parse("1.0.1"),
+    "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
 }
 
 
diff --git a/tools/filters/wiggle_to_simple.py b/tools/filters/wiggle_to_simple.py
index f1fcf045c8f..d619a8dc3f7 100755
--- a/tools/filters/wiggle_to_simple.py
+++ b/tools/filters/wiggle_to_simple.py
@@ -10,38 +10,20 @@ import sys
 
 import bx.wiggle
 
-from galaxy.util.ucsc import UCSCLimitException, UCSCOutWrapper
-
-
-def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+from galaxy.util.ucsc import (
+    UCSCLimitException,
+    UCSCOutWrapper
+)
 
 
 def main():
-    if len(sys.argv) > 1:
-        in_file = open(sys.argv[1])
-    else:
-        in_file = open(sys.stdin)
-
-    if len(sys.argv) > 2:
-        out_file = open(sys.argv[2], "w")
-    else:
-        out_file = sys.stdout
-
-    try:
-        for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
-            out_file.write("%s\n" % "\t".join(map(str, fields)))
-    except UCSCLimitException:
-        # Wiggle data was truncated, at the very least need to warn the user.
-        print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
-    except ValueError as e:
-        in_file.close()
-        out_file.close()
-        stop_err(str(e))
-
-    in_file.close()
-    out_file.close()
+    with open(sys.argv[1]) as in_file, open(sys.argv[2], "w") as out_file:
+        try:
+            for fields in bx.wiggle.IntervalReader(UCSCOutWrapper(in_file)):
+                out_file.write("%s\n" % "\t".join(map(str, fields)))
+        except UCSCLimitException:
+            # Wiggle data was truncated, at the very least need to warn the user.
+            sys.stderr.write('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
 
 
 if __name__ == "__main__":
diff --git a/tools/filters/wiggle_to_simple.xml b/tools/filters/wiggle_to_simple.xml
index 991ce655148..b4362369cae 100644
--- a/tools/filters/wiggle_to_simple.xml
+++ b/tools/filters/wiggle_to_simple.xml
@@ -1,6 +1,10 @@
-<tool id="wiggle2simple1" name="Wiggle-to-Interval" version="1.0.0">
+<tool id="wiggle2simple1" name="Wiggle-to-Interval" version="1.0.1" profile="16.04">
   <description>converter</description>
-  <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
+  <requirements>
+    <requirement type="package" version="19.09">galaxy-util</requirement>
+    <requirement type="package" version="0.8.6">bx-python</requirement>
+  </requirements>
+  <command>python '$__tool_directory__/wiggle_to_simple.py' '$input' '$out_file1'</command>
   <inputs>
     <param format="wig" name="input" type="data" label="Convert"/>
   </inputs>

From 05e8117995801ee1ac201ffc33a76e59265f5f51 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 11:59:30 +0100
Subject: [PATCH 74/96] Move aggregate_scores_in_intervals2 out of
 GALAXY_LIB_TOOLS_UNVERSIONED

---
 lib/galaxy/tools/__init__.py                         | 2 +-
 tools/maf/interval_maf_to_merged_fasta.py            | 3 +--
 tools/stats/aggregate_binned_scores_in_intervals.xml | 6 +++++-
 tools/stats/aggregate_scores_in_intervals.py         | 3 +--
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 66a58102a1a..c65e80bef05 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -130,7 +130,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "laj_1",
     "gff2bed1",
     "gff_filter_by_feature_count",
-    "aggregate_scores_in_intervals2",
     "Interval_Maf_Merged_Fasta2",
     "GeneBed_Maf_Fasta2",
     "maf_stats1",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "join1": packaging.version.parse("2.1.3"),
     "wiggle2simple1": packaging.version.parse("1.0.1"),
     "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
+    "aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
 }
 
 
diff --git a/tools/maf/interval_maf_to_merged_fasta.py b/tools/maf/interval_maf_to_merged_fasta.py
index 54ad28a4156..6df4bc88cdf 100644
--- a/tools/maf/interval_maf_to_merged_fasta.py
+++ b/tools/maf/interval_maf_to_merged_fasta.py
@@ -35,8 +35,7 @@ from galaxy.tools.util import maf_utilities
 
 
 def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(msg)
 
 
 def __main__():
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml
index 7e204c8ef67..fa8e1d111d8 100644
--- a/tools/stats/aggregate_binned_scores_in_intervals.xml
+++ b/tools/stats/aggregate_binned_scores_in_intervals.xml
@@ -1,5 +1,9 @@
-<tool id="aggregate_scores_in_intervals2" name="Aggregate datapoints" version="1.1.3">
+<tool id="aggregate_scores_in_intervals2" name="Aggregate datapoints" version="1.1.4" profile="16.04">
   <description>Appends the average, min, max of datapoints per interval</description>
+  <requirements>
+    <requirement type="package" version="19.09">galaxy-util</requirement>
+    <requirement type="package" version="0.8.6">bx-python</requirement>
+  </requirements>
   <command>
 python '$__tool_directory__/aggregate_scores_in_intervals.py'
 #if $score_source_type.score_source == "user"
diff --git a/tools/stats/aggregate_scores_in_intervals.py b/tools/stats/aggregate_scores_in_intervals.py
index 9c0cceba15b..2c5e8d7ad45 100755
--- a/tools/stats/aggregate_scores_in_intervals.py
+++ b/tools/stats/aggregate_scores_in_intervals.py
@@ -99,8 +99,7 @@ class FileBinnedArrayDir(Mapping):
 
 
 def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(msg)
 
 
 def load_scores_wiggle(fname, chrom_buffer_size=3):

From 418ca3d6cc6afef4b27e4f0fd8d34eff2311cd4d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 12:19:58 +0100
Subject: [PATCH 75/96] Use text mode in maf_utilites, set non-zero exit code

I don't see any binary formats being handled here, but strings are being
written to file handles in binary mode, so this should be correct.

Would be great to move maf_utilities out so that tools can depend
on this explicitly.
---
 lib/galaxy/datatypes/util/maf_utilities.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/util/maf_utilities.py b/lib/galaxy/datatypes/util/maf_utilities.py
index 3a5aa531bb2..c013dc215da 100644
--- a/lib/galaxy/datatypes/util/maf_utilities.py
+++ b/lib/galaxy/datatypes/util/maf_utilities.py
@@ -58,8 +58,7 @@ def get_species_in_block(block):
 
 
 def tool_fail(msg="Unknown Error"):
-    print("Fatal Error: %s" % msg, file=sys.stderr)
-    sys.exit()
+    sys.exit("Fatal Error: %s" % msg)
 
 
 class TempFileHandler(object):
@@ -103,11 +102,11 @@ class TempFileHandler(object):
                         else:
                             raise e
                 tmp_file.close()
-                self.files.append(open(filename, 'w+b'))
+                self.files.append(open(filename, 'w'))
             else:
                 while True:
                     try:
-                        self.files[index] = open(self.files[index].name, 'r+b')
+                        self.files[index] = open(self.files[index].name, 'r')
                         break
                     except OSError as e:
                         if self.open_file_indexes and e.errno == EMFILE:

From 2297b6ffdfa2b0a0adad0e0ddce5cab622ddc1be Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 12:35:25 +0100
Subject: [PATCH 76/96] Move CONVERTER_fastq_to_fqtoc0 out of
 GALAXY_LIB_TOOLS_UNVERSIONED

---
 .../datatypes/converters/fastq_to_fqtoc.py    | 28 ++++++++-----------
 .../datatypes/converters/fastq_to_fqtoc.xml   |  5 +++-
 lib/galaxy/tools/__init__.py                  |  2 +-
 3 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
index 5a90201de8f..f6cab4c12fe 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
@@ -20,30 +20,26 @@ def main():
     """
     input_fname = sys.argv[1]
     if is_gzip(input_fname):
-        print('Conversion is only possible for uncompressed files')
-        sys.exit(1)
-
-    out_file = open(sys.argv[2], 'w')
+        sys.exit('Conversion is only possible for uncompressed files')
 
     current_line = 0
     sequences = 1000000
     lines_per_chunk = 4 * sequences
     chunk_begin = 0
 
-    in_file = open(input_fname)
+    with open(input_fname) as in_file, open(sys.argv[2], 'w') as out_file:
+        out_file.write('{"sections" : [')
 
-    out_file.write('{"sections" : [')
+        for line in in_file:
+            current_line += 1
+            if 0 == current_line % lines_per_chunk:
+                chunk_end = in_file.tell()
+                out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences))
+                chunk_begin = chunk_end
 
-    for line in in_file:
-        current_line += 1
-        if 0 == current_line % lines_per_chunk:
-            chunk_end = in_file.tell()
-            out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences))
-            chunk_begin = chunk_end
-
-    chunk_end = in_file.tell()
-    out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4))
-    out_file.write(']}\n')
+        chunk_end = in_file.tell()
+        out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4))
+        out_file.write(']}\n')
 
 
 if __name__ == "__main__":
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
index d8bb8ad377f..7b039aa94b0 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
@@ -1,4 +1,7 @@
-<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.0" hidden="true">
+<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.1" hidden="true" profile="16.04">
+    <requirements>
+        <requirement type="package" version="19.09">galaxy-util</requirement>
+    </requirements>
     <command>python '$__tool_directory__/fastq_to_fqtoc.py' '$input1' '$output1'</command>
     <inputs>
         <param format="fastq" name="input1" type="data" label="Choose FASTQ file"/>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index c65e80bef05..32e66b3dd68 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -144,7 +144,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "maf_by_block_number1",
     # Converters
     "CONVERTER_bed_to_fli_0",
-    "CONVERTER_fastq_to_fqtoc0",
     "CONVERTER_gff_to_fli_0",
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "wiggle2simple1": packaging.version.parse("1.0.1"),
     "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
     "aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
+    "CONVERTER_fastq_to_fqtoc0": packaging.version.parse("1.0.1"),
 }
 
 

From fcb1a9d2c72c6630d22d212eb553df095d915d93 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 9 Feb 2020 12:36:41 +0100
Subject: [PATCH 77/96] Move CONVERTER_tar_to_directory out of
 GALAXY_LIB_TOOLS_UNVERSIONED

---
 lib/galaxy/datatypes/converters/tar_to_directory.xml | 5 ++++-
 lib/galaxy/tools/__init__.py                         | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/tar_to_directory.xml b/lib/galaxy/datatypes/converters/tar_to_directory.xml
index 6865b86ee1d..2bc27a0ef72 100644
--- a/lib/galaxy/datatypes/converters/tar_to_directory.xml
+++ b/lib/galaxy/datatypes/converters/tar_to_directory.xml
@@ -1,5 +1,8 @@
-<tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.0" profile="17.05">
+<tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.1" profile="17.05">
     <!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; -->
+    <requirements>
+        <requirement type="package" version="19.09">galay-util</requirement>
+    </requirements>
     <command>
         mkdir '$output1.files_path';
         cd '$output1.files_path';
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 32e66b3dd68..0adf06cc1ae 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -148,7 +148,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",
     "CONVERTER_maf_to_interval_0",
-    "CONVERTER_tar_to_directory",
     # Tools improperly migrated to the tool shed (devteam)
     "qualityFilter",
     "winSplitter",
@@ -191,6 +190,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "CONVERTER_wiggle_to_interval_0": packaging.version.parse("1.0.1"),
     "aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
     "CONVERTER_fastq_to_fqtoc0": packaging.version.parse("1.0.1"),
+    "CONVERTER_tar_to_directory": packaging.version.parse("1.0.1"),
 }
 
 

From ef7d5fb79e24982fcc9312aa23f380e2fa2b1ba3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 11:23:59 +0100
Subject: [PATCH 78/96] Figure out which tools are datatype converters

---
 lib/galaxy/datatypes/registry.py | 2 ++
 lib/galaxy/tools/__init__.py     | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 036bd1a82d4..0336c5cb2ac 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -45,6 +45,7 @@ class Registry(object):
         self.datatype_converters = OrderedDict()
         # Converters defined in local datatypes_conf.xml
         self.converters = []
+        self.converter_tools = set()
         # Converters defined in datatypes_conf.xml included in installed tool shed repositories.
         self.proprietary_converters = []
         self.converter_deps = {}
@@ -612,6 +613,7 @@ class Registry(object):
             try:
                 config_path = os.path.join(converter_path, tool_config)
                 converter = toolbox.load_tool(config_path, use_cached=use_cached)
+                self.converter_tools.add(converter)
                 if installed_repository_dict:
                     # If the converter is included in an installed tool shed repository, set the tool
                     # shed related tool attributes.
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 80ab77170f7..506ea1bdd57 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -526,6 +526,10 @@ class Tool(Dictifiable):
         tool_versions = self.tool_versions
         return not tool_versions or self.version == self.tool_versions[-1]
 
+    @property
+    def is_datatype_converter(self):
+        return self in self.app.datatypes_registry.converter_tools
+
     @property
     def tool_shed_repository(self):
         # If this tool is included in an installed tool shed repository, return it.

From 19703421a163eaf21bc3858a5c7646baf758f028 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 12:02:01 +0100
Subject: [PATCH 79/96] Skip datatype converter tests

---
 lib/galaxy/webapps/galaxy/api/tools.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index ad4f918e0ba..90208e09da8 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -172,15 +172,16 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         """
         test_counts_by_tool = {}
         for id, tool in self.app.toolbox.tools():
-            tests = tool.tests
-            if tests:
-                if tool.id not in test_counts_by_tool:
-                    test_counts_by_tool[tool.id] = {}
-                available_versions = test_counts_by_tool[tool.id]
-                available_versions[tool.version] = {
-                    "tool_name": tool.name,
-                    "count": len(tests),
-                }
+            if not tool.is_datatype_converter:
+                tests = tool.tests
+                if tests:
+                    if tool.id not in test_counts_by_tool:
+                        test_counts_by_tool[tool.id] = {}
+                    available_versions = test_counts_by_tool[tool.id]
+                    available_versions[tool.version] = {
+                        "tool_name": tool.name,
+                        "count": len(tests),
+                    }
         return test_counts_by_tool
 
     @expose_api_raw_anonymous_and_sessionless

From 06f470385b474df931cb2dbe872a78c686f693c6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 12:09:42 +0100
Subject: [PATCH 80/96] Test datatype converters in github workflow using
 planemo and biocontainers

---
 .github/workflows/converter_tests.yaml | 27 ++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 .github/workflows/converter_tests.yaml

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
new file mode 100644
index 00000000000..731bfb7de5a
--- /dev/null
+++ b/.github/workflows/converter_tests.yaml
@@ -0,0 +1,27 @@
+name: Converter tests
+on: [push, pull_request]
+jobs:
+
+  test:
+    name: Test
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache venv dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+    - name: Install planemo
+      run: pip install planemo
+    - name: Run tests
+      run: 'planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root .  lib/galaxy/datatypes/converters/*xml'

From 9e46d3bcae025921f371e23fb337159d6ac8557f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 12:19:54 +0100
Subject: [PATCH 81/96] Skip biocontainers, len file appears inaccessible

---
 .github/workflows/converter_tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 731bfb7de5a..4d0bf759ccc 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -24,4 +24,4 @@ jobs:
     - name: Install planemo
       run: pip install planemo
     - name: Run tests
-      run: 'planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root .  lib/galaxy/datatypes/converters/*xml'
+      run: 'planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root .  lib/galaxy/datatypes/converters/*xml'

From 624becffa97b1245651283ed97c9232728879a7c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 12:22:14 +0100
Subject: [PATCH 82/96] Prepare test data

---
 .github/workflows/converter_tests.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml
index 4d0bf759ccc..a8cd3f3f7a4 100644
--- a/.github/workflows/converter_tests.yaml
+++ b/.github/workflows/converter_tests.yaml
@@ -21,6 +21,8 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+    - name: fetch test data
+      run: git clone https://github.com/galaxyproject/galaxy-test-data && cp -R galaxy-test-data/* test-data
     - name: Install planemo
       run: pip install planemo
     - name: Run tests

From 33539d4bcf327b6e0288b110dd9f96ec14a11fc7 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 12:33:05 +0100
Subject: [PATCH 83/96] Drop unused array_tree code and converter

Couldn't find any use for array_tree in the codebase,
and these converters aren't loaded.
---
 .../bedgraph_to_array_tree_converter.py       | 58 -------------------
 .../bedgraph_to_array_tree_converter.xml      | 21 -------
 .../wiggle_to_array_tree_converter.py         | 31 ----------
 .../wiggle_to_array_tree_converter.xml        | 15 -----
 4 files changed, 125 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
 delete mode 100644 lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
 delete mode 100644 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
 delete mode 100644 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
deleted file mode 100644
index c2f90247eec..00000000000
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import division
-
-import sys
-
-from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
-
-BLOCK_SIZE = 100
-
-
-class BedGraphReader(object):
-    def __init__(self, f):
-        self.f = f
-
-    def __iter__(self):
-        return self
-
-    def __next__(self):
-        while True:
-            line = self.f.readline()
-            if not line:
-                raise StopIteration()
-            if line.isspace():
-                continue
-            if line[0] == "#":
-                continue
-            if line[0].isalpha():
-                if line.startswith("track") or line.startswith("browser"):
-                    continue
-
-                feature = line.strip().split()
-                chrom = feature[0]
-                chrom_start = int(feature[1])
-                chrom_end = int(feature[2])
-                score = float(feature[3])
-                return chrom, chrom_start, chrom_end, None, score
-
-
-def main():
-    input_fname = sys.argv[1]
-    out_fname = sys.argv[2]
-
-    with open(input_fname) as in_fh:
-        reader = BedGraphReader(in_fh)
-
-        # Fill array from reader
-        d = array_tree_dict_from_reader(reader, {}, block_size=BLOCK_SIZE)
-
-        for array_tree in d.values():
-            array_tree.root.build_summary()
-
-        with open(out_fname, 'w') as out:
-            FileArrayTreeDict.dict_to_file(d, out)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
deleted file mode 100644
index 013ee18e468..00000000000
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<tool id="CONVERTER_BedGraph_0" name="Index BedGraph for Track Viewer" version="1.0.1" hidden="true" profile="16.04">
-    <!-- Used internally to generate track indexes -->
-    <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
-    </requirements>
-    <command>python '$__tool_directory__/bedgraph_to_array_tree_converter.py' '$input' '$output'</command>
-    <inputs>
-        <param format="bedgraph" name="input" type="data" label="Choose BedGraph"/>
-    </inputs>
-    <outputs>
-        <data format="array_tree" name="output"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" format="bedgraph" value="gtf2bedgraph_out.bedgraph"/>
-            <output name="output" format="array_tree" value="gtf2array_tree_out.array_tree"/>
-        </test>
-    </tests>
-    <help>
-    </help>
-</tool>
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
deleted file mode 100644
index 12ed7a14af1..00000000000
--- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import division
-
-import sys
-
-from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
-from bx.arrays.wiggle import WiggleReader
-
-BLOCK_SIZE = 100
-
-
-def main():
-
-    input_fname = sys.argv[1]
-    out_fname = sys.argv[2]
-
-    with input(input_fname) as in_fh, open(out_fname, 'w') as out:
-        reader = WiggleReader(in_fh)
-
-        # Fill array from reader
-        d = array_tree_dict_from_reader(reader, {}, block_size=BLOCK_SIZE)
-
-        for array_tree in d.values():
-            array_tree.root.build_summary()
-
-        FileArrayTreeDict.dict_to_file(d, out)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
deleted file mode 100644
index f15b12e7b33..00000000000
--- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<tool id="CONVERTER_Wiggle_0" name="Index Wiggle for Track Viewer" version="1.0.1" hidden="true" profile="16.04">
-    <!-- Used internally to generate track indexes -->
-    <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
-    </requirements>
-    <command>python '$__tool_directory__/wiggle_to_array_tree_converter.py' '$input' '$output'</command>
-    <inputs>
-        <param format="wiggle" name="input" type="data" label="Choose wiggle"/>
-    </inputs>
-    <outputs>
-        <data format="array_tree" name="output"/>
-    </outputs>
-    <help>
-    </help>
-</tool>

From fe8790325938cc38406bf9d839cb2baa765d80fa Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 13:42:03 +0100
Subject: [PATCH 84/96] Index is binary

---
 .../converters/interval_to_interval_index_converter.py          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
index 29b727e5f53..5826a0edd31 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
@@ -44,7 +44,7 @@ def main():
         index.add(chrom, chrom_start, chrom_end, offset)
         offset += len(line)
 
-    with open(output_fname, 'w') as out:
+    with open(output_fname, 'wb') as out:
         index.write(out)
 
 

From 3d60bbf4d9a7d3f3ee917aee1be0da2b66022346 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 13:59:25 +0100
Subject: [PATCH 85/96] Load gff_to_bgzip_converter.xml, fixes
 gff_to_tabix_converter test

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample         | 1 +
 lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index a085297fb9f..75bff794326 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -142,6 +142,7 @@
       <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
       <converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <converter file="gff_to_fli_converter.xml" target_datatype="fli"/>
+      <converter file="gff_to_bgzip_converter.xml" target_datatype="bgzip"/>
       <display file="ensembl/ensembl_gff.xml" inherit="true"/>
       <display file="igv/gff.xml" inherit="true"/>
       <!-- <display file="gbrowse/gbrowse_gff.xml" inherit="true" /> -->
diff --git a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
index bb5fbbe1345..06ffce81787 100644
--- a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
@@ -14,6 +14,7 @@
     <tests>
         <test>
             <param name="input1" format="gff" value="gff_filter_by_feature_count_out2.gff"/>
+            <param name="bgzip" format="gff.gz" value="gff_filter_by_feature_count_out2.gff"/>
             <output name="output1" format="tabix" value="tabix_filter_by_feature_count_out2.tabix"/>
         </test>
     </tests>

From 18a46a7f35906f0f8e92f424dc7040c21b5745d6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 14:06:04 +0100
Subject: [PATCH 86/96] Update all datatype converters to use bx-python 0.8.7

---
 .../datatypes/converters/bed_to_interval_index_converter.xml | 2 +-
 .../datatypes/converters/interval_to_bed12_converter.xml     | 3 +--
 .../datatypes/converters/interval_to_bed6_converter.xml      | 3 +--
 lib/galaxy/datatypes/converters/interval_to_bed_converter.py | 3 +--
 .../datatypes/converters/interval_to_bed_converter.xml       | 5 ++---
 .../datatypes/converters/interval_to_bedstrict_converter.xml | 3 +--
 lib/galaxy/datatypes/converters/interval_to_coverage.xml     | 2 +-
 .../converters/interval_to_interval_index_converter.xml      | 2 +-
 .../converters/pileup_to_interval_index_converter.xml        | 2 +-
 .../datatypes/converters/vcf_to_interval_index_converter.xml | 2 +-
 10 files changed, 11 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
index 8f8f9eda906..60a06dc7753 100644
--- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bed_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_interval_index_converter.py' '$input1' '$output1'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index 7507c53a231..e98a8f46d7d 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -1,8 +1,7 @@
 <tool id="CONVERTER_interval_to_bed12_0" name="Convert Genomic Intervals To Strict BED12" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
-        <requirement type="package" version="3.6">python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_bedstrict_converter.py'
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index 2a966a2190a..f28f2a0f754 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -1,8 +1,7 @@
 <tool id="CONVERTER_interval_to_bed6_0" name="Convert Genomic Intervals To Strict BED6" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
-        <requirement type="package" version="3.6">python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
index 38fc4ed3679..57505520611 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py
@@ -10,8 +10,7 @@ assert sys.version_info[:2] >= (2, 6)
 
 
 def stop_err(msg):
-    sys.stderr.write(msg)
-    sys.exit()
+    sys.exit(msg)
 
 
 def __main__():
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
index 2ae06465195..4883b5e3dab 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
@@ -1,8 +1,7 @@
-<tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED" version="1.0.0">
+<tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bed_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index 76685a8178e..07a4f140167 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -1,8 +1,7 @@
 <tool id="CONVERTER_interval_to_bedstrict_0" name="Convert Genomic Intervals To Strict BED" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
-        <requirement type="package" version="3.6">python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.xml b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
index 9166f885054..b3636ca49b9 100644
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_coverage_0" name="Convert Genomic Intervals To COVERAGE" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_coverage.py' '$input1' '$output1'
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
index 5cde6aeb1a4..aaecd8ca53f 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_interval_index_0" name="Convert Interval to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_interval_index_converter.py'
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
index 66030851b71..7f33398966f 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/pileup_to_interval_index_converter.py'
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
index b74f0cd844a..627b297c328 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description>
     <requirements>
-        <requirement type="package" version="0.8.6">bx-python</requirement>
+        <requirement type="package" version="0.8.7">bx-python</requirement>
         <requirement type="package" version="1.1.4">galaxy_sequence_utils</requirement>
     </requirements>
     <command>python '$__tool_directory__/vcf_to_interval_index_converter.py' '$input1' '$output1'</command>

From 9fd8f74654b5ec6f216ffb089acdb2ddd3b2175e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 14:07:23 +0100
Subject: [PATCH 87/96] Bump bx-python core dependncy

---
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 2104230a1a2..0a0e79ba11f 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -28,7 +28,7 @@ boltons==19.3.0
 boto3==1.9.114
 boto==2.49.0
 botocore==1.12.253
-bx-python==0.8.6
+bx-python==0.8.7
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
 cachetools==3.1.1

From 97e667596248cb7efb2503ffc665d2aff6877037 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 14:11:24 +0100
Subject: [PATCH 88/96] Drop unused sam_to_bam converter

---
 lib/galaxy/datatypes/converters/sam_to_bam.py | 117 ------------------
 .../datatypes/converters/sam_to_bam.xml       |  26 ----
 2 files changed, 143 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/converters/sam_to_bam.py
 delete mode 100644 lib/galaxy/datatypes/converters/sam_to_bam.xml

diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.py b/lib/galaxy/datatypes/converters/sam_to_bam.py
deleted file mode 100644
index 66962d13392..00000000000
--- a/lib/galaxy/datatypes/converters/sam_to_bam.py
+++ /dev/null
@@ -1,117 +0,0 @@
-#!/usr/bin/env python
-# Dan Blankenberg
-
-"""
-A wrapper script for converting SAM to BAM, with sorting.
-%prog input_filename.sam output_filename.bam
-"""
-import optparse
-import os
-import shutil
-import subprocess
-import sys
-import tempfile
-
-import packaging.version
-
-CHUNK_SIZE = 2 ** 20  # 1mb
-
-
-def cleanup_before_exit(tmp_dir):
-    if tmp_dir and os.path.exists(tmp_dir):
-        shutil.rmtree(tmp_dir)
-
-
-def cmd_exists(cmd):
-    # http://stackoverflow.com/questions/5226958/which-equivalent-function-in-python
-    for path in os.environ["PATH"].split(":"):
-        if os.path.exists(os.path.join(path, cmd)):
-            return True
-    return False
-
-
-def _get_samtools_version():
-    version = '0.0.0'
-    if not cmd_exists('samtools'):
-        raise Exception('This tool needs samtools, but it is not on PATH.')
-    # Get the version of samtools via --version-only, if available
-    p = subprocess.Popen(['samtools', '--version-only'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    output, error = p.communicate()
-    # --version-only is available
-    # Format is <version x.y.z>+htslib-<a.b.c>
-    if p.returncode == 0:
-        version = output.split('+')[0]
-        return version
-
-    output = subprocess.Popen(['samtools'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[1]
-    lines = output.split('\n')
-    for line in lines:
-        if line.lower().startswith('version'):
-            # Assuming line looks something like: version: 0.1.12a (r862)
-            version = line.split()[1]
-            break
-    return version
-
-
-def __main__():
-    # Parse Command Line
-    parser = optparse.OptionParser()
-    (options, args) = parser.parse_args()
-
-    assert len(args) == 2, 'You must specify the input and output filenames'
-    input_filename, output_filename = args
-
-    tmp_dir = tempfile.mkdtemp(prefix='tmp-sam_to_bam_converter-')
-
-    # convert to SAM
-    unsorted_bam_filename = os.path.join(tmp_dir, 'unsorted.bam')
-    unsorted_stderr_filename = os.path.join(tmp_dir, 'unsorted.stderr')
-    proc = subprocess.Popen(['samtools', 'view', '-bS', input_filename],
-                            stdout=open(unsorted_bam_filename, 'wb'),
-                            stderr=open(unsorted_stderr_filename, 'wb'),
-                            cwd=tmp_dir)
-    return_code = proc.wait()
-    if return_code:
-        stderr_target = sys.stderr
-    else:
-        stderr_target = sys.stdout
-    with open(unsorted_stderr_filename) as stderr:
-        while True:
-            chunk = stderr.read(CHUNK_SIZE)
-            if chunk:
-                stderr_target.write(chunk)
-            else:
-                break
-
-    # sort sam, so indexing will not fail
-    sorted_stderr_filename = os.path.join(tmp_dir, 'sorted.stderr')
-    sorting_prefix = os.path.join(tmp_dir, 'sorted_bam')
-    # samtools changed sort command arguments (starting from version 1.3)
-    samtools_version = packaging.version.parse(_get_samtools_version())
-    if samtools_version < packaging.version.parse('1.0'):
-        sort_args = ['-o', unsorted_bam_filename, sorting_prefix]
-    else:
-        sort_args = ['-T', sorting_prefix, unsorted_bam_filename]
-    proc = subprocess.Popen(['samtools', 'sort'] + sort_args,
-                            stdout=open(output_filename, 'wb'),
-                            stderr=open(sorted_stderr_filename, 'wb'),
-                            cwd=tmp_dir)
-    return_code = proc.wait()
-
-    if return_code:
-        stderr_target = sys.stderr
-    else:
-        stderr_target = sys.stdout
-    with open(sorted_stderr_filename) as stderr:
-        while True:
-            chunk = stderr.read(CHUNK_SIZE)
-            if chunk:
-                stderr_target.write(chunk)
-            else:
-                break
-
-    cleanup_before_exit(tmp_dir)
-
-
-if __name__ == "__main__":
-    __main__()
diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.xml b/lib/galaxy/datatypes/converters/sam_to_bam.xml
deleted file mode 100644
index f77feec0663..00000000000
--- a/lib/galaxy/datatypes/converters/sam_to_bam.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<tool id="CONVERTER_sam_to_bam" name="Convert SAM to BAM" version="2.0.0">
-    <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-    <!-- Used on the metadata edit page. -->
-    <!-- FIXME: conversion will only work if headers for reference sequences are in input file.
-         To fix this: (a) merge sam_to_bam tool in tools with this conversion (like fasta_to_len 
-         conversion); and (b) define a datatype-specific way to set converter parameters.
-      -->
-    <requirements>
-        <requirement type="package">samtools</requirement>
-    </requirements>
-    <command>python '$__tool_directory__/sam_to_bam.py' '$input1' '$output'</command>
-    <inputs>
-        <param name="input1" type="data" format="sam" label="SAM file"/>
-    </inputs>
-    <outputs>
-        <data name="output" format="bam"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" format="sam" value="bfast_out1.sam"/>
-            <output name="output" format="bam" value="bfast_out1.bam"/>
-        </test>
-    </tests>
-    <help>
-    </help>
-</tool>

From 570228dce8287e33d01f794299c755722ef40333 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 12 Feb 2020 14:14:11 +0100
Subject: [PATCH 89/96] Fix *_to_interval_index converter scripts

---
 .../interval_to_interval_index_converter.py   | 19 ++++++++++---------
 .../pileup_to_interval_index_converter.py     | 15 ++++++++-------
 .../vcf_to_interval_index_converter.py        | 18 ++++++++++--------
 3 files changed, 28 insertions(+), 24 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
index 5826a0edd31..c5f7b72cb85 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
@@ -33,16 +33,17 @@ def main():
     # Do conversion.
     index = Indexes()
     offset = 0
-    for line in open(input_fname, "r"):
-        feature = line.strip().split()
-        if not feature or feature[0].startswith("track") or feature[0].startswith("#"):
+    with open(input_fname) as in_fh:
+        for line in in_fh:
+            feature = line.strip().split()
+            if not feature or feature[0].startswith("track") or feature[0].startswith("#"):
+                offset += len(line)
+                continue
+            chrom = feature[options.chrom_col]
+            chrom_start = int(feature[options.start_col])
+            chrom_end = int(feature[options.end_col])
+            index.add(chrom, chrom_start, chrom_end, offset)
             offset += len(line)
-            continue
-        chrom = feature[options.chrom_col]
-        chrom_start = int(feature[options.start_col])
-        chrom_end = int(feature[options.end_col])
-        index.add(chrom, chrom_start, chrom_end, offset)
-        offset += len(line)
 
     with open(output_fname, 'wb') as out:
         index.write(out)
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
index 3fb7f1f4ccf..103e0c5f4ba 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
@@ -22,14 +22,15 @@ def main():
     # Do conversion.
     index = Indexes()
     offset = 0
-    for line in open(input_fname, "r"):
-        chrom, start = line.split()[0:2]
-        # Pileup format is 1-based.
-        start = int(start) - 1
-        index.add(chrom, start, start + 1, offset)
-        offset += len(line)
+    with open(input_fname) as in_fh:
+        for line in in_fh:
+            chrom, start = line.split()[0:2]
+            # Pileup format is 1-based.
+            start = int(start) - 1
+            index.add(chrom, start, start + 1, offset)
+            offset += len(line)
 
-    with open(output_fname, 'w') as out:
+    with open(output_fname, 'wb') as out:
         index.write(out)
 
 
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
index a635db88aab..8f5e24402af 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
@@ -18,15 +18,17 @@ def main():
 
     # Do conversion.
     index = Indexes()
-    reader = galaxy_utils.sequence.vcf.Reader(open(in_file))
-    offset = reader.metadata_len
-    for vcf_line in reader:
-        # VCF format provides a chrom and 1-based position for each variant.
-        # IntervalIndex expects 0-based coordinates.
-        index.add(vcf_line.chrom, vcf_line.pos - 1, vcf_line.pos, offset)
-        offset += len(vcf_line.raw_line)
+    with open(in_file) as in_fh:
+        reader = galaxy_utils.sequence.vcf.Reader(in_fh)
+        offset = reader.metadata_len
+        for vcf_line in reader:
+            # VCF format provides a chrom and 1-based position for each variant.
+            # IntervalIndex expects 0-based coordinates.
+            index.add(vcf_line.chrom, vcf_line.pos - 1, vcf_line.pos, offset)
+            offset += len(vcf_line.raw_line)
 
-    index.write(open(out_file, "w"))
+    with open(out_file, "wb") as out_fh:
+        index.write(out_fh)
 
 
 if __name__ == "__main__":

From 316931bdf901e0db0677fad057d12fc5ed024384 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 12 Feb 2020 13:17:55 -0500
Subject: [PATCH 90/96] Fix styleguide for new webpack config approach.

---
 client/styleguide.config.js | 42 ++++++++++++++++++++-----------------
 client/webpack.config.js    |  2 +-
 2 files changed, 24 insertions(+), 20 deletions(-)

diff --git a/client/styleguide.config.js b/client/styleguide.config.js
index d3d7d64d7e9..98d07952f49 100644
--- a/client/styleguide.config.js
+++ b/client/styleguide.config.js
@@ -2,8 +2,9 @@ const path = require("path");
 const glob = require("glob");
 const fs = require("fs");
 const merge = require("webpack-merge");
+const baseConfig = require("./webpack.config.js")
 
-let webpackConfig = require("./webpack.config.js");
+const webpackConfig = baseConfig();
 
 const fileLoaderTest = /\.(png|jpg|jpeg|gif|svg|woff|woff2|ttf|eot)(\?.*$|$)/;
 
@@ -37,9 +38,9 @@ const fileLoaderConfigRule = { rules: [{ test: fileLoaderTest, use: ["file-loade
 webpackConfig.module = merge.smart(webpackConfig.module, fileLoaderConfigRule);
 webpackConfig.output.publicPath = "";
 
-webpackConfig.resolve.modules.push( path.join(__dirname, "galaxy/style/scss") );
+webpackConfig.resolve.modules.push(path.join(__dirname, "galaxy/style/scss"));
 
-galaxyStyleDocs = []
+const galaxyStyleDocs = [];
 glob.sync("./galaxy/docs/galaxy-*.md").forEach(file => {
     const name = file.match(/galaxy-(\w+).md/)[1];
     galaxyStyleDocs.push({ name: name, content: file });
@@ -47,26 +48,29 @@ glob.sync("./galaxy/docs/galaxy-*.md").forEach(file => {
 
 const sections = [
     {
-	name: 'Components',
-	// Components that are directories will get their own section
-	sections: glob.sync("./galaxy/scripts/components/*").map(file => {
-	    if (fs.lstatSync(file).isDirectory()) {
-		return {
-		    name: path.basename(file),
-		    components: file + "/**/*.vue"
-		};
-	    }
-	}).filter( v => v ),
-	// ...while top level components are handled here.
-	components: './galaxy/scripts/components/*.vue',
+        name: "Components",
+        // Components that are directories will get their own section
+        sections: glob
+            .sync("./galaxy/scripts/components/*")
+            .map(file => {
+                if (fs.lstatSync(file).isDirectory()) {
+                    return {
+                        name: path.basename(file),
+                        components: file + "/**/*.vue"
+                    };
+                }
+            })
+            .filter(v => v),
+        // ...while top level components are handled here.
+        components: "./galaxy/scripts/components/*.vue"
     },
     {
-	name: 'Galaxy styles',
-	sections: galaxyStyleDocs
+        name: "Galaxy styles",
+        sections: galaxyStyleDocs
     },
     {
-	name: "Basic Bootstrap Styles",
-	content: "./galaxy/docs/bootstrap.md"
+        name: "Basic Bootstrap Styles",
+        content: "./galaxy/docs/bootstrap.md"
     }
 ];
 
diff --git a/client/webpack.config.js b/client/webpack.config.js
index bd341ad0b4d..7e2044c2f31 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -16,7 +16,7 @@ module.exports = (env = {}, argv = {}) => {
     // environment name based on -d, -p, webpack flag
     const targetEnv = argv.mode || "development";
 
-    let buildconfig = {
+    const buildconfig = {
         entry: {
             login: ["polyfills", "bundleEntries", "entry/login"],
             analysis: ["polyfills", "bundleEntries", "entry/analysis"],

From 83150b334a408133c93bba2e40b62c0f447020c1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 12 Feb 2020 13:50:40 -0500
Subject: [PATCH 91/96] Reorder sections, drop uncategorized components
 temporarily.

---
 client/styleguide.config.js | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/client/styleguide.config.js b/client/styleguide.config.js
index 98d07952f49..3bd12aeee16 100644
--- a/client/styleguide.config.js
+++ b/client/styleguide.config.js
@@ -47,6 +47,14 @@ glob.sync("./galaxy/docs/galaxy-*.md").forEach(file => {
 });
 
 const sections = [
+    {
+        name: "Galaxy styles",
+        sections: galaxyStyleDocs
+    },
+    {
+        name: "Basic Bootstrap Styles",
+        content: "./galaxy/docs/bootstrap.md"
+    },
     {
         name: "Components",
         // Components that are directories will get their own section
@@ -62,15 +70,7 @@ const sections = [
             })
             .filter(v => v),
         // ...while top level components are handled here.
-        components: "./galaxy/scripts/components/*.vue"
-    },
-    {
-        name: "Galaxy styles",
-        sections: galaxyStyleDocs
-    },
-    {
-        name: "Basic Bootstrap Styles",
-        content: "./galaxy/docs/bootstrap.md"
+        //components: "./galaxy/scripts/components/*.vue"
     }
 ];
 

From 2c23c11506360553df23de595e2307b3349077c8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 12 Feb 2020 14:00:04 -0500
Subject: [PATCH 92/96] reincorporate toplevel components

---
 client/styleguide.config.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/styleguide.config.js b/client/styleguide.config.js
index 3bd12aeee16..511dc134efc 100644
--- a/client/styleguide.config.js
+++ b/client/styleguide.config.js
@@ -70,7 +70,7 @@ const sections = [
             })
             .filter(v => v),
         // ...while top level components are handled here.
-        //components: "./galaxy/scripts/components/*.vue"
+        components: "./galaxy/scripts/components/*.vue"
     }
 ];
 

From 003108f927c7ee62b6920110c9334d8803457c28 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 13 Feb 2020 16:04:02 +0100
Subject: [PATCH 93/96] Drop unused interval_to_coverage converter

---
 .../converters/interval_to_coverage.py        | 151 ------------------
 .../converters/interval_to_coverage.xml       |  25 ---
 2 files changed, 176 deletions(-)
 delete mode 100644 lib/galaxy/datatypes/converters/interval_to_coverage.py
 delete mode 100644 lib/galaxy/datatypes/converters/interval_to_coverage.xml

diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.py b/lib/galaxy/datatypes/converters/interval_to_coverage.py
deleted file mode 100644
index aff6b296a11..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.py
+++ /dev/null
@@ -1,151 +0,0 @@
-#!/usr/bin/env python
-"""
-Converter to generate 3 (or 4) column base-pair coverage from an interval file.
-
-usage: %prog bed_file out_file
-    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in interval file
-    -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in coverage file
-"""
-import subprocess
-import tempfile
-from bisect import bisect
-from os import environ
-
-from bx.cookbook import doc_optparse
-from bx.intervals import io
-
-INTERVAL_METADATA = ('chromCol',
-                     'startCol',
-                     'endCol',
-                     'strandCol',)
-
-COVERAGE_METADATA = ('chromCol',
-                     'positionCol',
-                     'forwardCol',
-                     'reverseCol',)
-
-
-def main(interval, coverage):
-    """
-    Uses a sliding window of partitions to count coverages.
-    Every interval record adds its start and end to the partitions.  The result
-    is a list of partitions, or every position that has a (maybe) different
-    number of basepairs covered.  We don't worry about merging because we pop
-    as the sorted intervals are read in.  As the input start positions exceed
-    the partition positions in partitions, coverages are kicked out in bulk.
-    """
-    partitions = []
-    forward_covs = []
-    reverse_covs = []
-    chrom = None
-    lastchrom = None
-    for record in interval:
-        chrom = record.chrom
-        if lastchrom and not lastchrom == chrom and partitions:
-            for partition in range(0, len(partitions) - 1):
-                forward = forward_covs[partition]
-                reverse = reverse_covs[partition]
-                if forward + reverse > 0:
-                    coverage.write(chrom=chrom, position=range(partitions[partition], partitions[partition + 1]),
-                                   forward=forward, reverse=reverse)
-            partitions = []
-            forward_covs = []
-            reverse_covs = []
-
-        start_index = bisect(partitions, record.start)
-        forward = int(record.strand == "+")
-        reverse = int(record.strand == "-")
-        forward_base = 0
-        reverse_base = 0
-        if start_index > 0:
-            forward_base = forward_covs[start_index - 1]
-            reverse_base = reverse_covs[start_index - 1]
-        partitions.insert(start_index, record.start)
-        forward_covs.insert(start_index, forward_base)
-        reverse_covs.insert(start_index, reverse_base)
-        end_index = bisect(partitions, record.end)
-        for index in range(start_index, end_index):
-            forward_covs[index] += forward
-            reverse_covs[index] += reverse
-        partitions.insert(end_index, record.end)
-        forward_covs.insert(end_index, forward_covs[end_index - 1] - forward)
-        reverse_covs.insert(end_index, reverse_covs[end_index - 1] - reverse)
-
-        if partitions:
-            for partition in range(0, start_index):
-                forward = forward_covs[partition]
-                reverse = reverse_covs[partition]
-                if forward + reverse > 0:
-                    coverage.write(chrom=chrom, position=range(partitions[partition], partitions[partition + 1]),
-                                   forward=forward, reverse=reverse)
-            partitions = partitions[start_index:]
-            forward_covs = forward_covs[start_index:]
-            reverse_covs = reverse_covs[start_index:]
-
-        lastchrom = chrom
-
-    # Finish the last chromosome
-    if partitions:
-        for partition in range(0, len(partitions) - 1):
-            forward = forward_covs[partition]
-            reverse = reverse_covs[partition]
-            if forward + reverse > 0:
-                coverage.write(chrom=chrom, position=range(partitions[partition], partitions[partition + 1]),
-                               forward=forward, reverse=reverse)
-
-
-class CoverageWriter(object):
-    def __init__(self, out_stream=None, chromCol=0, positionCol=1, forwardCol=2, reverseCol=3):
-        self.out_stream = out_stream
-        self.reverseCol = reverseCol
-        self.nlines = 0
-        positions = {str(chromCol): '%(chrom)s',
-                     str(positionCol): '%(position)d',
-                     str(forwardCol): '%(forward)d',
-                     str(reverseCol): '%(reverse)d'}
-        if reverseCol < 0:
-            self.template = "%(0)s\t%(1)s\t%(2)s\n" % positions
-        else:
-            self.template = "%(0)s\t%(1)s\t%(2)s\t%(3)s\n" % positions
-
-    def write(self, **kwargs):
-        if self.reverseCol < 0:
-            kwargs['forward'] += kwargs['reverse']
-        posgen = kwargs['position']
-        for position in posgen:
-            kwargs['position'] = position
-            self.out_stream.write(self.template % kwargs)
-
-    def close(self):
-        self.out_stream.flush()
-        self.out_stream.close()
-
-
-if __name__ == "__main__":
-    options, args = doc_optparse.parse(__doc__)
-    try:
-        chr_col_1, start_col_1, end_col_1, strand_col_1 = [int(x) - 1 for x in options.cols1.split(',')]
-        chr_col_2, position_col_2, forward_col_2, reverse_col_2 = [int(x) - 1 for x in options.cols2.split(',')]
-        in_fname, out_fname = args
-    except Exception:
-        doc_optparse.exception()
-
-    # Sort through a tempfile first
-    with tempfile.NamedTemporaryFile(mode="r") as temp_file:
-        environ['LC_ALL'] = 'POSIX'
-        subprocess.check_call([
-            'sort', '-f', '-n', '-k', chr_col_1 + 1, '-k', start_col_1 + 1, '-k', end_col_1 + 1, '-o', temp_file.name, in_fname
-        ])
-
-        coverage = CoverageWriter(out_stream=open(out_fname, "a"),
-                                  chromCol=chr_col_2, positionCol=position_col_2,
-                                  forwardCol=forward_col_2, reverseCol=reverse_col_2, )
-        temp_file.seek(0)
-        interval = io.NiceReaderWrapper(temp_file,
-                                        chrom_col=chr_col_1,
-                                        start_col=start_col_1,
-                                        end_col=end_col_1,
-                                        strand_col=strand_col_1,
-                                        fix_strand=True)
-        main(interval, coverage)
-    coverage.close()
diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.xml b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
deleted file mode 100644
index b3636ca49b9..00000000000
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<tool id="CONVERTER_interval_to_coverage_0" name="Convert Genomic Intervals To COVERAGE" version="1.0.1" profile="16.04">
-    <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-    <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
-    </requirements>
-    <command>
-        python '$__tool_directory__/interval_to_coverage.py' '$input1' '$output1'
-        -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
-        -2 ${output1.metadata.chromCol},${output1.metadata.positionCol},${output1.metadata.forwardCol},${output1.metadata.reverseCol}
-    </command>
-    <inputs>
-        <param format="interval" name="input1" type="data" label="Choose intervals"/>
-    </inputs>
-    <outputs>
-        <data format="coverage" name="output1"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" format="interval" value="2.interval"/>
-            <output name="output1" format="coverage" value="2.coverage"/>
-        </test>
-    </tests>
-    <help>
-    </help>
-</tool>

From cd7a2c3418d6540ab3bb3177b0b0216c54ebff56 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 13 Feb 2020 16:04:24 +0100
Subject: [PATCH 94/96] Bump bx-python to 0.8.8

---
 .../datatypes/converters/bed_to_interval_index_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml | 2 +-
 lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/interval_to_bed_converter.xml   | 2 +-
 .../datatypes/converters/interval_to_bedstrict_converter.xml    | 2 +-
 .../converters/interval_to_interval_index_converter.xml         | 2 +-
 .../datatypes/converters/pileup_to_interval_index_converter.xml | 2 +-
 .../datatypes/converters/vcf_to_interval_index_converter.xml    | 2 +-
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
index 60a06dc7753..98618ef4c68 100644
--- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bed_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_interval_index_converter.py' '$input1' '$output1'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index e98a8f46d7d..ace96313d74 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed12_0" name="Convert Genomic Intervals To Strict BED12" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_bedstrict_converter.py'
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index f28f2a0f754..77f39d8dfa9 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed6_0" name="Convert Genomic Intervals To Strict BED6" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
index 4883b5e3dab..5ff627e8174 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED" version="1.0.0" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bed_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index 07a4f140167..33203ae06d6 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bedstrict_0" name="Convert Genomic Intervals To Strict BED" version="1.0.1" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/interval_to_bedstrict_converter.py' '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
index aaecd8ca53f..9c8d1a949c4 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_interval_index_0" name="Convert Interval to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/interval_to_interval_index_converter.py'
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
index 7f33398966f..7b960385095 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
     </requirements>
     <command>
         python '$__tool_directory__/pileup_to_interval_index_converter.py'
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
index 627b297c328..9c2c96fa559 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.1" hidden="true" profile="16.04">
     <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description>
     <requirements>
-        <requirement type="package" version="0.8.7">bx-python</requirement>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
         <requirement type="package" version="1.1.4">galaxy_sequence_utils</requirement>
     </requirements>
     <command>python '$__tool_directory__/vcf_to_interval_index_converter.py' '$input1' '$output1'</command>
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 0a0e79ba11f..06a75a494d7 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -28,7 +28,7 @@ boltons==19.3.0
 boto3==1.9.114
 boto==2.49.0
 botocore==1.12.253
-bx-python==0.8.7
+bx-python==0.8.8
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
 cachetools==3.1.1

From 33f528a07acbc382224a9df9fb73db43ee8da10d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 30 Jan 2020 18:25:15 -0500
Subject: [PATCH 95/96] parent fc713a3cd5f3398fa85f0c0502679a15027bdcef author
 Dannon Baker <dannon.baker@gmail.com> 1580426715 -0500 committer Dannon Baker
 <dannon.baker@gmail.com> 1581649360 -0500

Drop bower exclusion from babel-loader.

We need to transpile bootstrap-vue, otherwise edge blows up.

Edge can't handle two events on the same element (?!?!?!) and silently
just doesn't fire change when there's also an input binding here?

Update commentary for babel stage excludes

Add IMask functionality for initial input masking (similar to previous functionality, but a little more robust).  We may want to work on the regex here.

Fix unused var/eslint

Adjust karma's webpack config to completely ignore node-modules for transpilation, fixes it messing with bootstrap-vue and failing

Client format...
---
 client/galaxy/scripts/mvc/ui/ui-slider.js | 30 +++++++++++++----------
 client/karma/webpack.config.unittest.js   |  5 ++++
 client/webpack.config.js                  | 11 +++++----
 3 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/client/galaxy/scripts/mvc/ui/ui-slider.js b/client/galaxy/scripts/mvc/ui/ui-slider.js
index f1050baf374..b60d956725b 100644
--- a/client/galaxy/scripts/mvc/ui/ui-slider.js
+++ b/client/galaxy/scripts/mvc/ui/ui-slider.js
@@ -1,4 +1,5 @@
 import Backbone from "backbone";
+import IMask from "imask";
 
 import Utils from "utils/utils";
 
@@ -23,20 +24,23 @@ const View = Backbone.View.extend({
         this.$text = this.$(".ui-form-slider-text");
         this.$slider = this.$(".ui-form-slider-element");
 
-        // add text field event
-        this.$text
-            .on("change", e => {
-                this.value(e.currentTarget.value);
-            })
-            .on("input", e => {
-                const input = e.currentTarget;
-                if (this._isParameter(input.value)) {
-                    return;
-                } else if (!this.model.get("precise")) {
-                    input.value = input.value.split(".")[0];
+        IMask(this.$text[0], {
+            mask: value => {
+                if (this._isParameter(value)) {
+                    return true;
                 }
-                input.value = input.value.replace(/[^0-9eE.-]/g, "");
-            });
+                if (!this.model.get("precise")) {
+                    if (value != value.split(".")[0]) {
+                        return false;
+                    }
+                }
+                return value == value.replace(/[^0-9eE.-]/g, "");
+            }
+        });
+
+        this.$text[0].addEventListener("change", e => {
+            this.value(e.currentTarget.value);
+        });
 
         // build slider, cannot be rebuild in render
         const opts = this.model.attributes;
diff --git a/client/karma/webpack.config.unittest.js b/client/karma/webpack.config.unittest.js
index b8df1e6ff0f..63466d2b093 100644
--- a/client/karma/webpack.config.unittest.js
+++ b/client/karma/webpack.config.unittest.js
@@ -36,9 +36,14 @@ module.exports = (env, argv) => {
     // Using babel-plugin-rewire to handle dependency mocking since webpack 4
     // exports immutable bindings for ES modules but we still need a way to
     // overwrite dependencies during unit-testing.
+    //
+    // Additionally, set exclude for babel-loader to completely ignore *all*
+    // node-modules, without our exceptions to support IE as in parent webpack
+    // config.
 
     wpConfig.module.rules = wpConfig.module.rules.map(rule => {
         if (rule.loader == "babel-loader") {
+            rule.exclude = [/(node_modules\/)/]
             rule.options.plugins.push("rewire");
         }
         return rule;
diff --git a/client/webpack.config.js b/client/webpack.config.js
index bd341ad0b4d..47d15f80b45 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -66,11 +66,12 @@ module.exports = (env = {}, argv = {}) => {
                 },
                 {
                     test: /\.js$/,
-                    // Pretty sure we don't want anything except node_modules here
-                    exclude: [
-                        /(node_modules\/(?!(handsontable)\/)|bower_components)/,
-                        libsBase
-                    ],
+                    /*
+                     * Babel transpile excludes for:
+                     * - all node_modules except for handsontable, bootstrap-vue
+                     * - statically included libs (like old jquery plugins, etc.)
+                    */
+                    exclude: [/(node_modules\/(?!(handsontable|bootstrap-vue)\/))/, libsBase],
                     loader: "babel-loader",
                     options: {
                         cacheDirectory: true,

From 4b1cd45c5bb2c686f2cfb14e6af22a1a510fb7bb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 18 Feb 2020 12:36:41 +0100
Subject: [PATCH 96/96] Prevent tool execution getting stuck in history when a
 chromInfo dataset is in paused state

If a chromInfo dataset is paused (or in other non-terminal states)
execution will not start until the dataset is ready, which may be never.
So instead we prefer datasets in OK state and ignore those that
will never be OK. In theory that may fix some odd issues where
jobs never start running.
---
 lib/galaxy/managers/context.py | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py
index d8fb528ee0b..6699b80432d 100644
--- a/lib/galaxy/managers/context.py
+++ b/lib/galaxy/managers/context.py
@@ -180,12 +180,24 @@ class ProvidesHistoryContext(object):
             # The API presents a Bunch for a history.  Until the API is
             # more fully featured for handling this, also return None.
             return None
-        datasets = self.sa_session.query(self.app.model.HistoryDatasetAssociation) \
-                                  .filter_by(deleted=False, history_id=self.history.id, extension="len")
+        non_ready_or_ok = set(self.app.model.Dataset.non_ready_states)
+        non_ready_or_ok.add(self.app.model.HistoryDatasetAssociation.states.OK)
+        datasets = self.sa_session.query(
+            self.app.model.HistoryDatasetAssociation
+        ).filter_by(
+            deleted=False,
+            history_id=self.history.id,
+            extension="len"
+        ).filter(
+            self.app.model.HistoryDatasetAssociation._state.in_(non_ready_or_ok),
+        )
+        valid_ds = None
         for ds in datasets:
-            if dbkey == ds.dbkey:
-                return ds
-        return None
+            if ds.dbkey == dbkey:
+                if ds.state == self.app.model.HistoryDatasetAssociation.states.OK:
+                    return ds
+                valid_ds = ds
+        return valid_ds
 
     @property
     def db_builds(self):