From 4c9100c5c29727b2b614901f038881a43fc99484 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 18 Feb 2020 20:26:02 +0100
Subject: [PATCH 1/5] Fix dependency for CONVERTER_tar_to_directory

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

diff --git a/lib/galaxy/datatypes/converters/tar_to_directory.xml b/lib/galaxy/datatypes/converters/tar_to_directory.xml
index ba4e21a81b7..c6af0c761e3 100644
--- a/lib/galaxy/datatypes/converters/tar_to_directory.xml
+++ b/lib/galaxy/datatypes/converters/tar_to_directory.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.1" profile="17.05">
     <!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; -->
     <requirements>
-        <requirement type="package" version="19.09">galay-util</requirement>
+        <requirement type="package" version="19.9">galay-util</requirement>
     </requirements>
     <command>
         mkdir '$output1.files_path';

From fb71055bfe9261378c35da4952cf97fe8b3105d3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 19 Feb 2020 09:56:02 +0100
Subject: [PATCH 2/5] Fix typo, other places that use wrong galaxy-util version

---
 lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml             | 2 +-
 lib/galaxy/datatypes/converters/tar_to_directory.xml           | 2 +-
 lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml | 2 +-
 tools/filters/wiggle_to_simple.xml                             | 2 +-
 tools/stats/aggregate_binned_scores_in_intervals.xml           | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
index ca11e91cc4e..a95fdf77b62 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.1" hidden="true" profile="16.04">
     <requirements>
-        <requirement type="package" version="19.09">galaxy-util</requirement>
+        <requirement type="package" version="19.9">galaxy-util</requirement>
     </requirements>
     <command>python '$__tool_directory__/fastq_to_fqtoc.py' '$input1' '$output1'</command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/tar_to_directory.xml b/lib/galaxy/datatypes/converters/tar_to_directory.xml
index c6af0c761e3..ed489eccb43 100644
--- a/lib/galaxy/datatypes/converters/tar_to_directory.xml
+++ b/lib/galaxy/datatypes/converters/tar_to_directory.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.1" profile="17.05">
     <!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; -->
     <requirements>
-        <requirement type="package" version="19.9">galay-util</requirement>
+        <requirement type="package" version="19.9">galaxy-util</requirement>
     </requirements>
     <command>
         mkdir '$output1.files_path';
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
index 0ed14968083..7f2a1beb659 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
@@ -2,7 +2,7 @@
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <requirements>
-      <requirement type="package" version="19.09">galaxy-util</requirement>
+      <requirement type="package" version="19.9">galaxy-util</requirement>
       <requirement type="package" version="0.8.6">bx-python</requirement>
     </requirements>
     <command>python '$__tool_directory__/wiggle_to_simple_converter.py' '$input' '$out_file1'</command>
diff --git a/tools/filters/wiggle_to_simple.xml b/tools/filters/wiggle_to_simple.xml
index b4362369cae..fc4fd390d87 100644
--- a/tools/filters/wiggle_to_simple.xml
+++ b/tools/filters/wiggle_to_simple.xml
@@ -1,7 +1,7 @@
 <tool id="wiggle2simple1" name="Wiggle-to-Interval" version="1.0.1" profile="16.04">
   <description>converter</description>
   <requirements>
-    <requirement type="package" version="19.09">galaxy-util</requirement>
+    <requirement type="package" version="19.9">galaxy-util</requirement>
     <requirement type="package" version="0.8.6">bx-python</requirement>
   </requirements>
   <command>python '$__tool_directory__/wiggle_to_simple.py' '$input' '$out_file1'</command>
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml
index fa8e1d111d8..1c710f8b198 100644
--- a/tools/stats/aggregate_binned_scores_in_intervals.xml
+++ b/tools/stats/aggregate_binned_scores_in_intervals.xml
@@ -1,7 +1,7 @@
 <tool id="aggregate_scores_in_intervals2" name="Aggregate datapoints" version="1.1.4" profile="16.04">
   <description>Appends the average, min, max of datapoints per interval</description>
   <requirements>
-    <requirement type="package" version="19.09">galaxy-util</requirement>
+    <requirement type="package" version="19.9">galaxy-util</requirement>
     <requirement type="package" version="0.8.6">bx-python</requirement>
   </requirements>
   <command>

From 8e7c7915ba9d4e9a881312bcd5da26c87f172a8b Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 19 Feb 2020 10:53:01 +0100
Subject: [PATCH 3/5] Adjust bx-python imports for
 https://github.com/bxlab/bx-python/commit/fd08da3b49e89e0accd2c372d4a99427628ce432

---
 lib/galaxy/datatypes/util/maf_utilities.py | 2 +-
 tools/maf/maf_to_bed.py                    | 5 +++--
 tools/maf/maf_to_bed.xml                   | 2 +-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/datatypes/util/maf_utilities.py b/lib/galaxy/datatypes/util/maf_utilities.py
index c013dc215da..4df2450aa28 100644
--- a/lib/galaxy/datatypes/util/maf_utilities.py
+++ b/lib/galaxy/datatypes/util/maf_utilities.py
@@ -45,7 +45,7 @@ def src_split(src):
 def src_merge(spec, chrom, contig=None):
     if None in [spec, chrom]:
         spec = chrom = spec or chrom
-    return bx.align.maf.src_merge(spec, chrom, contig)
+    return bx.align.src_merge(spec, chrom, contig)
 
 
 def get_species_in_block(block):
diff --git a/tools/maf/maf_to_bed.py b/tools/maf/maf_to_bed.py
index fdb59219886..e6116f2d864 100644
--- a/tools/maf/maf_to_bed.py
+++ b/tools/maf/maf_to_bed.py
@@ -9,6 +9,7 @@ import sys
 from collections import OrderedDict
 
 from bx.align import maf
+from bx.align.core import src_split
 
 
 def __main__():
@@ -28,7 +29,7 @@ def __main__():
         try:
             for i, m in enumerate(maf.Reader(open(input_filename, 'r'))):
                 for c in m.components:
-                    spec, chrom = maf.src_split(c.src)
+                    spec, chrom = src_split(c.src)
                     if not spec or not chrom:
                         spec = c.src
                     species[spec] = None
@@ -64,7 +65,7 @@ def __main__():
             if len(l) < num_species and partial == "partial_disallowed":
                 continue
             for c in l:
-                spec, chrom = maf.src_split(c.src)
+                spec, chrom = src_split(c.src)
                 if not spec or not chrom:
                     spec = chrom = c.src
                 if spec not in out_files.keys():
diff --git a/tools/maf/maf_to_bed.xml b/tools/maf/maf_to_bed.xml
index e7e56b6d32d..423a44412e0 100644
--- a/tools/maf/maf_to_bed.xml
+++ b/tools/maf/maf_to_bed.xml
@@ -1,4 +1,4 @@
-<tool id="MAF_To_BED1" name="MAF to BED" version="1.0.0">
+<tool id="MAF_To_BED1" name="MAF to BED" version="1.0.0" profile="16.04">
     <description>Converts a MAF formatted file to the BED format</description>
     <macros>
         <import>macros.xml</import>

From 22d58322569a814ab01736e3020ea2b4e13d5bf3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 19 Feb 2020 11:32:33 +0100
Subject: [PATCH 4/5] Fix tabular_to_dbnsfp dependency, move out of
 GALAXY_LIB_TOOLS

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

diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
index 5d61c6119a4..42f8db82126 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
@@ -1,7 +1,7 @@
 <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>
+        <requirement type="package" version="0.15.4">pysam</requirement>
     </requirements>
     <command>python '$__tool_directory__/tabular_to_dbnsfp.py' '$input' '$dbnsfp.extra_files_path/dbNSFP.gz'</command>
     <inputs>
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index cf980050fe1..222bfa7a949 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -159,8 +159,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "substitutions1",
     "find_diag_hits",
     "cufflinks",
-    # Tools improperly migrated to the tool shed (iuc)
-    "tabular_to_dbnsfp",
     # Tools improperly migrated using Galaxy (from shed other)
     "column_join",
     "gd_coverage_distributions",  # Genome Diversity tools from miller-lab
@@ -189,6 +187,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
     "CONVERTER_fastq_to_fqtoc0": packaging.version.parse("1.0.1"),
     "CONVERTER_tar_to_directory": packaging.version.parse("1.0.1"),
+    "tabular_to_dbnsfp": packaging.version.parse("1.0.1"),
 }
 
 

From 747eabdd2ec94a669ba6cd6722205ee2eca08016 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 19 Feb 2020 13:43:34 +0100
Subject: [PATCH 5/5] Fix tabular_to_dbnsfp  test data files

Input should be vcf-like, so let's just use a vcf
---
 lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
index 42f8db82126..ddb3a44fa95 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
@@ -12,8 +12,8 @@
     </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"/>
+            <param name="input" format="tabular" value="vcf2pgSnp_input.vcf"/>
+            <output name="dbnsfp" format="snpsiftdbnsfp" value="vcf2pgSnp_input.vcf.snpsiftdbnsfp"/>
         </test>
     </tests>
     <help>