Mercurial > repos > iuc > bwameth

comparison bwameth.xml @ 5:4895589b7dab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:36:22 -0400
parents 06e882075239
children 368c79aa228f
comparison
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4:06e882075239 5:4895589b7dab
76 #if $single_or_paired.single_or_paired_opts == 'single': 76 #if $single_or_paired.single_or_paired_opts == 'single':
77 $read1 77 $read1
78 #else: 78 #else:
79 $read1 $read2 79 $read1 $read2
80 #end if 80 #end if
81 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam - 81 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
82 ]]> 82 ]]>
83 </command> 83 </command>
84 <inputs> 84 <inputs>
85 <conditional name="referenceSource"> 85 <conditional name="referenceSource">
86 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> 86 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">