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Merge pull request #15053 from lldelisle/fix_converter_to_bgzip

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fix interval_to_bgzip for sub gff classes
This commit is contained in:
Nicola Soranzo
2022-11-24 14:15:09 +00:00
committed by GitHub
parent d935286b49 f8452c78ae
commit b0202d16da
2 changed files with 16 additions and 3 deletions
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lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+15 -3
View File
@@ -1,4 +1,4 @@
<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.1" hidden="true" profile="16.04">
<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to 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>
@@ -6,8 +6,12 @@
</requirements>
<command><![CDATA[
python '$__tool_directory__/bgzip.py'
#if $input1.ext in ['bed', 'gff', 'vcf']
-P $input1.ext
#if $input1.is_of_type('bed')
-P bed
#elif $input1.is_of_type('vcf')
-P vcf
#elif $input1.is_of_type('gff')
-P gff
#else
-c ${input1.metadata.chromCol}
-s ${input1.metadata.startCol}
@@ -47,6 +51,14 @@
<param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
<output name="output1" ftype="bgzip" value="bgzip_to_maf_in.bgzip"/>
</test>
<test>
<param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
<output name="output1" ftype="bgzip" >
<assert_contents>
<has_size value="270" delta="10" />
</assert_contents>
</output>
</test>
</tests>
<help>
</help>
lib/galaxy/tools/__init__.py
+1
View File
@@ -281,6 +281,7 @@ WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
"Show beginning1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.2")),
"Show tail1": safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
"sort1": safe_update(packaging.version.parse("1.1.0"), packaging.version.parse("1.2.0")),
"CONVERTER_interval_to_bgzip_0": safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.2")),
}