Mercurial > repos > iuc > bwa_mem2
diff bwa-mem2.xml @ 3:bfaa0d22c2e4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 689a4aeaf70a8e77be8589b1dcceb190f9df626a
| author | iuc |
|---|---|
| date | Wed, 26 Jul 2023 20:02:13 +0000 |
| parents | b4a22d90cce9 |
| children |
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--- a/bwa-mem2.xml Wed Nov 24 21:29:45 2021 +0000 +++ b/bwa-mem2.xml Wed Jul 26 20:02:13 2023 +0000 @@ -71,6 +71,9 @@ ${analysis_type.io_options.M} ${analysis_type.io_options.five} ${analysis_type.io_options.q} + #if str( $analysis_type.io_options.K ): + -K '${analysis_type.io_options.K}' + #end if #end if #end if @@ -238,7 +241,7 @@ </conditional> <conditional name="io_options"> - <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options."> + <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, -M, and -K options."> <option value="set">Set</option> <option value="do_not_set" selected="True">Do not set</option> </param> @@ -252,6 +255,7 @@ <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/> <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" /> <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard<1.96 compatibility" /> + <param name="K" type="integer" optional="True" label="Process this number of input bases in each batch regardless of nThreads (for reproducibility)" help="-K"/> </when> <when value="do_not_set"> <!-- do nothing -->