Mercurial > repos > iuc > varscan_somatic
diff varscan_somatic.xml @ 5:d37adcc2ec03 draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
author | iuc |
---|---|
date | Wed, 05 Dec 2018 11:16:52 -0500 |
parents | 2fe9ebb98aad |
children | 2c66c4025db2 |
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--- a/varscan_somatic.xml Tue Dec 04 05:53:45 2018 -0500 +++ b/varscan_somatic.xml Wed Dec 05 11:16:52 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1"> +<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.2"> <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description> <macros> <import>macros.xml</import> @@ -38,13 +38,13 @@ </stdio> <command><![CDATA[ #if str($reference.source) == "history": - #set ref_genome = 'ref.fa' + #set $ref_genome = 'ref.fa' ln -s -f '$reference.genome' $ref_genome && #else: - #set ref_genome = '$reference.genome.fields.path' + #set $ref_genome = str($reference.genome.fields.path) #end if - #set normal_data = 'normal.bam' - #set tumor_data = 'tumor.bam' + #set $normal_data = 'normal.bam' + #set $tumor_data = 'tumor.bam' ln -s -f '$normal_bam' $normal_data && ln -s -f '$tumor_bam' $tumor_data && ln -s -f '${normal_bam.metadata.bam_index}' ${normal_data}.bai && @@ -127,7 +127,7 @@ --max-mmqs-diff ${filter_params.max_mmqs_diff} #end if --verbose - $ref_genome + '$ref_genome' ]]></command> <inputs> @@ -304,6 +304,25 @@ <expand macro="test_mentions_filters" /> </output> </test> + <test expect_num_outputs="1"> + <conditional name="reference"> + <param name="source" value="cached" /> + <param name="genome" value="hg19mito" /> + </conditional> + <param name="normal_bam" dbkey="hg19" value="control_chrM.bam" /> + <param name="tumor_bam" dbkey="hg19" value="tumor_chrM.bam" /> + <param name="split_output" value="false" /> + <conditional name="call_params"> + <param name="settings" value="varscan_defaults" /> + </conditional> + <conditional name="filter_params"> + <param name="settings" value="varscan_defaults" /> + </conditional> + <output name="output"> + <expand macro="test_mentions_contig" /> + <expand macro="test_mentions_filters" /> + </output> + </test> <test expect_num_outputs="2"> <conditional name="reference"> <param name="source" value="history" />