Mercurial > repos > iuc > umi_tools_dedup

comparison umi-tools_dedup.xml @ 9:a289db9d3bbc draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:25:42 -0400
parents ec7b02a30ed3
children 0ac9b15f11c2
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8:746615d72e00 9:a289db9d3bbc
32 #end if 32 #end if
33 #if $input.is_of_type("sam"): 33 #if $input.is_of_type("sam"):
34 --in-sam 34 --in-sam
35 #end if 35 #end if
36 -I '$input_file' -S deduped.bam && 36 -I '$input_file' -S deduped.bam &&
37 samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -o '$output' -O BAM 37 samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
38 ]]></command> 38 ]]></command>
39 <inputs> 39 <inputs>
40 <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" /> 40 <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" />
41 <param name="extract_umi_method" argument="--extract-umi-method" type="select"> 41 <param name="extract_umi_method" argument="--extract-umi-method" type="select">
42 <option value="read_id" selected="True">Read ID</option> 42 <option value="read_id" selected="True">Read ID</option>