Mercurial > repos > iuc > samtools_coverage
diff samtools_coverage.xml @ 2:8883a04ba181 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
| author | iuc |
|---|---|
| date | Wed, 31 May 2023 17:15:08 +0000 |
| parents | c25ce26fb975 |
| children | f052a4f6e358 |
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--- a/samtools_coverage.xml Mon Aug 15 09:07:53 2022 +0000 +++ b/samtools_coverage.xml Wed May 31 17:15:08 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>computes the depth at each position or region</description> <macros> <import>macros.xml</import> @@ -7,11 +7,15 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @PREPARE_IDX@ + #if $condition_input.input_pooling == "No": + @PREPARE_IDX@ + #else: + @PREPARE_IDX_MULTIPLE@ + #end if samtools coverage #if $condition_input.input_pooling == "Yes": - ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input] ) } + ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input_bams] ) } #else '$condition_input.input' #end if @@ -22,11 +26,11 @@ #set $filter = $additional_options.required_flags @FLAGS@ - -rf $flags + --rf $flags #set $filter = $additional_options.skipped_flags @FLAGS@ - -ff $flags + --ff $flags #if $condition_histogram.histogram_select == "yes" -m @@ -45,10 +49,10 @@ <option value="Yes">Yes</option> </param> <when value="No" > - <param name="input" type="data" format="bam" multiple="true" label="BAM file"/> + <param name="input" type="data" format="bam" label="BAM file"/> </when> <when value="Yes"> - <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> + <param name="input_bams" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> </when> </conditional> @@ -96,7 +100,7 @@ </test> <test> <param name="input_pooling" value="Yes" /> - <param name="input" value="test_1.bam,test_2.bam" ftype="bam" /> + <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> <param name="histogram_select" value="yes" /> <param name="n_bins" value="100" /> <output name="output" file="results_3.txt" ftype="tabular" />