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comparison macs2_bdgbroadcall.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 f5d67c722d67
children 640d3af5d833
comparison
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8:e8a060164e11 9:acbd3fb47f90
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="4.1.3">gawk</requirement> 7 <requirement type="package" version="4.1.3">gawk</requirement>
8 </expand> 8 </expand>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command> 11 <command><![CDATA[
12 <![CDATA[ 12 @home_dir@
13 macs2 bdgbroadcall 13 macs2 bdgbroadcall
14 --ifile '${ infile }' 14 --ifile '${ infile }'
15 --cutoff-peak '${ cutoffpeak }' 15 --cutoff-peak '${ cutoffpeak }'
16 --cutoff-link '${ cutofflink }' 16 --cutoff-link '${ cutofflink }'
17 --min-length '${ minlen }' 17 --min-length '${ minlen }'
18 --lvl1-max-gap '${ LVL1MAXGAP }' 18 --lvl1-max-gap '${ LVL1MAXGAP }'
19 --lvl2-max-gap '${ LVL2MAXGAP }' 19 --lvl2-max-gap '${ LVL2MAXGAP }'
20 --ofile "macs2_bdgbroadcall.bdg" 20 --ofile "macs2_bdgbroadcall.bdg"
21 && 21 &&
22 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }' 22 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
23 ]]> 23 ]]></command>
24 </command>
25 <inputs> 24 <inputs>
26 <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" /> 25 <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
27 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" 26 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
28 help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/> 27 help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/>
29 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" 28 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"