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comparison macs2_bdgpeakcall.xml @ 2:bfe57d6e0c4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
author iuc
date Mon, 12 Oct 2015 11:24:39 -0400
parents fe62ba547975
children beb902da6e5f
comparison
equal deleted inserted replaced
1:859c982b1f7f 2:bfe57d6e0c4c
1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0"> 1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0">
2 <description>Call peaks from bedGraph output</description> 2 <description>Call peaks from bedGraph output</description>
3 <macros>
4 <import>macs2_macros.xml</import>
5 </macros>
3 <expand macro="requirements"> 6 <expand macro="requirements">
4 <requirement type="package" version="4.1.0">gnu_awk</requirement> 7 <requirement type="package" version="4.1.0">gnu_awk</requirement>
5 </expand> 8 </expand>
9 <expand macro="stdio" />
6 <expand macro="version_command" /> 10 <expand macro="version_command" />
7 <macros>
8 <import>macs2_macros.xml</import>
9 </macros>
10 <command> 11 <command>
11 macs2 bdgpeakcall 12 macs2 bdgpeakcall
12 --ifile "${ infile }" 13 --ifile "${ infile }"
13 --cutoff "${ cutoff }" 14 --cutoff "${ cutoff }"
14 --min-length "${ minlen }" 15 --min-length "${ minlen }"
17 ${ notrackline } 18 ${ notrackline }
18 --ofile "macs2_bdgpeakcall.bdg" 19 --ofile "macs2_bdgpeakcall.bdg"
19 &amp;&amp; 20 &amp;&amp;
20 awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }" 21 awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }"
21 </command> 22 </command>
22 <expand macro="stdio" />
23 <inputs> 23 <inputs>
24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> 24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
25 25
26 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" 26 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
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: 5.0 (--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: 5.0 (--cutoff)"/>
28 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/> 28 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/>
29 <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/> 29 <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/>
30 30
31 <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" 31 <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
32 label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region." 32 label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region."
33 help="(-call-summits)"/> 33 help="(-call-summits)"/>
34 <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" 34 <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False"
35 label="Include trackline into bedGraph output" 35 label="Include trackline into bedGraph output"
36 help="required by USCS (--no-trackline)"/> 36 help="required by USCS (--no-trackline)"/>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> 39 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />