Mercurial > repos > iuc > macs2
diff macs2_bdgbroadcall.xml @ 36:8c8ae1e19b10 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:46:49 -0400 |
| parents | c82a1f154c60 |
| children | 1b3f899ef044 |
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--- a/macs2_bdgbroadcall.xml Wed Apr 29 12:06:24 2015 -0400 +++ b/macs2_bdgbroadcall.xml Mon May 04 22:46:49 2015 -0400 @@ -1,12 +1,13 @@ <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="4.1.0">gnu_awk</requirement> </expand> + <expand macro="stdio" /> <expand macro="version_command" /> - <macros> - <import>macs2_macros.xml</import> - </macros> <command> macs2 bdgbroadcall --ifile "${ infile }" @@ -19,18 +20,17 @@ && awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }" </command> - <expand macro="stdio" /> <inputs> <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> - <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" + <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" help="Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. default: 2.0 (--cutoff-peak)"/> - <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" + <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" + <param name="minlen" type="integer" label="Minimum length of peak" value="200" help="It is recommended to set it as d value." /> - <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" + <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" help="It is recommended to set it to tag size" /> - <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" + <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" /> </inputs> <outputs>