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] 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"),
 }