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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
author | iuc |
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date | Wed, 27 Dec 2017 10:18:03 -0500 |
parents | f5d67c722d67 |
children | acbd3fb47f90 |
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<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0"> <description>Call broad peaks from bedGraph output</description> <macros> <import>macs2_macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="4.1.3">gawk</requirement> </expand> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ macs2 bdgbroadcall --ifile '${ infile }' --cutoff-peak '${ cutoffpeak }' --cutoff-link '${ cutofflink }' --min-length '${ minlen }' --lvl1-max-gap '${ LVL1MAXGAP }' --lvl2-max-gap '${ LVL2MAXGAP }' --ofile "macs2_bdgbroadcall.bdg" && awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }' ]]> </command> <inputs> <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" /> <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/> <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. Default=1 (--cutoff-link)"/> <param name="minlen" type="integer" label="Minimum length of peak" value="200" help="It is recommended to set it as d value. Default=200 (--min-length)" /> <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" /> <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" /> </inputs> <outputs> <data name="outfile" format="interval" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" /> <param name="cutoffpeak" value="2.0"/> <param name="cutofflink" value="1.0"/> <param name="minlen" value="200"/> <param name="LVL1MAXGAP" value="30"/> <param name="LVL2MAXGAP" value="800"/> <output name="outfile" file="bdgbroadcall_output.bdg"/> </test> </tests> <help> **What it does** This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2. .. _MACS2: https://github.com/taoliu/MACS @citation@ </help> <expand macro="citations" /> </tool>