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comparison macs2_refinepeak.xml @ 9:acbd3fb47f90 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
author iuc
date Thu, 25 Jan 2018 02:11:52 -0500
parents beb902da6e5f
children 424aefbd7777
comparison
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8:e8a060164e11 9:acbd3fb47f90
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 @home_dir@
11 macs2 refinepeak 11 macs2 refinepeak
12 -b '${ bed_infile }' 12 -b '${ bed_infile }'
13 -i '${ infile }' 13 -i '${ infile }'
14 --format '${ infile.extension.upper() }' 14 --format '${ infile.extension.upper() }'
15 --cutoff '${ cutoff }' 15 --cutoff '${ cutoff }'
16 --window-size '${ winsize }' 16 --window-size '${ winsize }'
17 --ofile '${ outfile }' 17 --ofile '${ outfile }'
18 ]]> 18 ]]></command>
19 </command>
20 <inputs> 19 <inputs>
21 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> 20 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
22 <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> 21 <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
23 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/> 22 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
24 <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" /> 23 <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />