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mvdbeek
2025-03-12 12:40:57 +01:00
parent 21f1fc9db2
commit 773301a679
1 changed files with 9 additions and 3 deletions
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lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
+9 -3
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@@ -5,7 +5,7 @@
</requirements>
<command><![CDATA[
ln -s '$bgzip' input.bgz &&
tabix
tabix
#if $input1.is_of_type('bed')
-p bed
#elif $input1.is_of_type('vcf')
@@ -23,7 +23,7 @@
if [ ! -s input.bgz.tbi ]; then
>&2 echo "The converted tabix index file is empty, meaning the input data is invalid.";
exit 1;
fi
fi
&&
tabix -l input.bgz
]]></command>
@@ -41,6 +41,7 @@
<tests>
<test>
<param name="input1" ftype="bed" value="droPer1.bed"/>
<param name="bgzip" ftype="bgzip" value="droPer1.bed.gz"/>
<output name="output1" ftype="tabix">
<assert_contents>
<has_size value="133"/>
@@ -55,6 +56,7 @@
</test>
<test>
<param name="input1" ftype="encodepeak" value="encode.broad.peak"/>
<param name="bgzip" ftype="bgzip" value="encode.broad.peak.gz"/>
<output name="output1" ftype="tabix">
<assert_contents>
<has_size value="110" delta="10"/>
@@ -69,6 +71,7 @@
</test>
<test>
<param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>
<param name="bgzip" ftype="bgzip" value="gff_filter_by_feature_count_out2.gff.gz"/>
<output name="output1" ftype="tabix">
<assert_contents>
<has_size value="120"/>
@@ -83,6 +86,7 @@
</test>
<test>
<param name="input1" ftype="interval" value="2.interval"/>
<param name="bgzip" ftype="bgzip" value="2.interval.gz"/>
<output name="output1" ftype="tabix">
<assert_contents>
<has_size value="247"/>
@@ -97,6 +101,7 @@
</test>
<test>
<param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>
<param name="bgzip" ftype="bgzip" value="vcf_to_maf_in.vcf.gz"/>
<output name="output1" ftype="tabix">
<assert_contents>
<has_size value="143"/>
@@ -111,6 +116,7 @@
</test>
<test>
<param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>
<param name="bgzip" ftype="bgzip" value="cufflinks_out1.gtf.gz"/>
<output name="output1" ftype="tabix">
<assert_contents>
<has_size value="125"/>
@@ -119,7 +125,7 @@
<assert_command>
<has_text text="-p gff"/>
</assert_command>
</test>
</test>
</tests>
<help>
</help>