Mercurial > repos > iuc > umi_tools_group

comparison umi-tools_group.xml @ 10:a24f5b991320 draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:27:38 -0400
parents f73f13641bb6
children 30c3906fbf43
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9:3b8fecdf9058 10:a24f5b991320
36 #if $input.is_of_type("sam"): 36 #if $input.is_of_type("sam"):
37 --in-sam 37 --in-sam
38 #end if 38 #end if
39 --output-bam 39 --output-bam
40 -I '$input_file' -S grouped.bam && 40 -I '$input_file' -S grouped.bam &&
41 samtools sort grouped.bam -@ \${GALAXY_SLOTS:-1} -o '$output' -O BAM 41 samtools sort grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <param name="input" type="data" format="sam,bam" label="Reads to group in SAM or BAM format" /> 44 <param name="input" type="data" format="sam,bam" label="Reads to group in SAM or BAM format" />
45 <param name="extract_umi_method" argument="--extract-umi-method" type="select"> 45 <param name="extract_umi_method" argument="--extract-umi-method" type="select">
46 <option value="read_id" selected="True">Read ID</option> 46 <option value="read_id" selected="True">Read ID</option>