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 01/72] 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 02/72] 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 03/72] 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 04/72] 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 05/72] 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 06/72] 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 07/72] 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 08/72] 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 09/72] 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 10/72] 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 11/72] 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 12/72] 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 13/72] 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 14/72] 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 15/72] 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 16/72] 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 17/72] 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 18/72] 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 19/72] 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 20/72] 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 21/72] 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 22/72] 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 23/72] 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 24/72] 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 25/72] 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 26/72] 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 27/72] 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 28/72] 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 29/72] 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 30/72] 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 31/72] 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 32/72] 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 33/72] 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 34/72] 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 35/72] 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 36/72] 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 37/72] 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 38/72] 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 39/72] 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 40/72] 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 41/72] 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 42/72] 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 43/72] 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 44/72] 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 45/72] 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 46/72] 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 47/72] 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 48/72] 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 49/72] 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 50/72] 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 51/72] 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 52/72] 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 53/72] 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 54/72] 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 55/72] 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 56/72] 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 57/72] 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 58/72] 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 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 59/72] 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 60/72] 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 61/72] 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 62/72] 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 63/72] 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 64/72] 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 65/72] 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 66/72] 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 67/72] 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 68/72] 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 69/72] 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 70/72] 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 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 71/72] 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 72/72] 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