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comparison macs2_bdgbroadcall.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
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1:859c982b1f7f 2:bfe57d6e0c4c
1 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0"> 1 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0">
2 <description>Call broad peaks from bedGraph output</description> 2 <description>Call broad 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 bdgbroadcall 12 macs2 bdgbroadcall
12 --ifile "${ infile }" 13 --ifile "${ infile }"
13 --cutoff-peak "${ cutoffpeak }" 14 --cutoff-peak "${ cutoffpeak }"
14 --cutoff-link "${ cutofflink }" 15 --cutoff-link "${ cutofflink }"
17 --lvl2-max-gap "${ LVL2MAXGAP }" 18 --lvl2-max-gap "${ LVL2MAXGAP }"
18 --ofile "macs2_bdgbroadcall.bdg" 19 --ofile "macs2_bdgbroadcall.bdg"
19 &amp;&amp; 20 &amp;&amp;
20 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }" 21 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ 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 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" 25 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
26 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)"/> 26 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)"/>
27 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" 27 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
28 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)"/> 28 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)"/>
29 <param name="minlen" type="integer" label="Minimum length of peak" value="200" 29 <param name="minlen" type="integer" label="Minimum length of peak" value="200"
30 help="It is recommended to set it as d value." /> 30 help="It is recommended to set it as d value." />
31 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" 31 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
32 help="It is recommended to set it to tag size" /> 32 help="It is recommended to set it to tag size" />
33 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" 33 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
34 help="It is recommended to set it to 4 times of d value" /> 34 help="It is recommended to set it to 4 times of d value" />
35 </inputs> 35 </inputs>
36 <outputs> 36 <outputs>
37 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> 37 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
38 </outputs> 38 </outputs>