Mercurial > repos > iuc > umi_tools_dedup
comparison umi-tools_dedup.xml @ 9:1692b1acebfd draft
"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author | iuc |
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date | Tue, 10 Sep 2019 14:28:24 -0400 |
parents | a6477bafd522 |
children | c6567483aa1e |
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8:983ec27dce7c | 9:1692b1acebfd |
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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> |