Mercurial > repos > devteam > samtools_calmd
diff samtools_calmd.xml @ 3:3d873744df7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
| author | iuc |
|---|---|
| date | Mon, 29 Jul 2019 08:47:41 -0400 |
| parents | e65c2cd0964c |
| children | 06dc50b7b711 |
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--- a/samtools_calmd.xml Fri Nov 30 17:46:15 2018 -0500 +++ b/samtools_calmd.xml Mon Jul 29 08:47:41 2019 -0400 @@ -7,23 +7,25 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - #if str( $reference_source.reference_source_selector ) == "history": - #set ref_fa = 'ref.fa' - ln -s '${reference_source.ref_fasta}' ref.fa && - samtools faidx ref.fa && - #else: - #set ref_fa = str( $reference_source.ref_fasta.fields.path ) - #end if +@ADDTHREADS@ +#if str( $reference_source.reference_source_selector ) == "history": + #set ref_fa = 'ref.fa' + ln -s '${reference_source.ref_fasta}' ref.fa && + samtools faidx ref.fa && +#else: + #set ref_fa = str( $reference_source.ref_fasta.fields.path ) +#end if - samtools calmd - $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq - #if str($option_set.option_sets) == 'advanced': - $option_set.change_identical -C $option_set.adjust_mq - #end if - -b - '$input_bam' - '$ref_fa' - > '$calmd_output' +samtools calmd + $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq + #if str($option_set.option_sets) == 'advanced': + $option_set.change_identical -C $option_set.adjust_mq + #end if + -b + -@ \$addthreads + '$input_bam' + '$ref_fa' + > '$calmd_output' ]]></command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />