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comparison macs2_bdgbroadcall.xml @ 5:beb902da6e5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:57 -0400
parents bfe57d6e0c4c
children f5d67c722d67
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4:56e104999978 5:beb902da6e5f
7 <requirement type="package" version="4.1.0">gnu_awk</requirement> 7 <requirement type="package" version="4.1.0">gnu_awk</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>
12 <![CDATA[
12 macs2 bdgbroadcall 13 macs2 bdgbroadcall
13 --ifile "${ infile }" 14 --ifile '${ infile }'
14 --cutoff-peak "${ cutoffpeak }" 15 --cutoff-peak '${ cutoffpeak }'
15 --cutoff-link "${ cutofflink }" 16 --cutoff-link '${ cutofflink }'
16 --min-length "${ minlen }" 17 --min-length '${ minlen }'
17 --lvl1-max-gap "${ LVL1MAXGAP }" 18 --lvl1-max-gap '${ LVL1MAXGAP }'
18 --lvl2-max-gap "${ LVL2MAXGAP }" 19 --lvl2-max-gap '${ LVL2MAXGAP }'
19 --ofile "macs2_bdgbroadcall.bdg" 20 --ofile "macs2_bdgbroadcall.bdg"
20 &amp;&amp; 21 &&
21 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }" 22 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
23 ]]>
22 </command> 24 </command>
23 <inputs> 25 <inputs>
24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> 26 <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
25 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" 27 <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)"/> 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 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" 29 <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)"/> 30 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" 31 <param name="minlen" type="integer" label="Minimum length of peak" value="200"
30 help="It is recommended to set it as d value." /> 32 help="It is recommended to set it as d value. Default=200 (--min-length)" />
31 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" 33 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
32 help="It is recommended to set it to tag size" /> 34 help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" />
33 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" 35 <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" /> 36 help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" />
35 </inputs> 37 </inputs>
36 <outputs> 38 <outputs>
37 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> 39 <data name="outfile" format="interval" label="${tool.name} on ${on_string}" />
38 </outputs> 40 </outputs>
39 <tests> 41 <tests>
40 <test> 42 <test>
41 <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> 43 <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" />
42 <param name="cutoffpeak" value="2.0"/> 44 <param name="cutoffpeak" value="2.0"/>
43 <param name="cutofflink" value="1.0"/> 45 <param name="cutofflink" value="1.0"/>
44 <param name="minlen" value="200"/> 46 <param name="minlen" value="200"/>
45 <param name="LVL1MAXGAP" value="30"/> 47 <param name="LVL1MAXGAP" value="30"/>
46 <param name="LVL2MAXGAP" value="800"/> 48 <param name="LVL2MAXGAP" value="800"/>
47 <output name="outfile" file="bdgbroadcall_on_callpeak_treatment.tabular"/> 49 <output name="outfile" file="bdgbroadcall_output.bdg"/>
48 </test> 50 </test>
49 </tests> 51 </tests>
50 <help> 52 <help>
51 **What it does** 53 **What it does**
52 54
53 Call broad peaks from bedGraph output. 55 This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.
54 bdgbroadcall from macs2 56
57 .. _MACS2: https://github.com/taoliu/MACS
58
55 59
56 @citation@ 60 @citation@
57 </help> 61 </help>
58 <expand macro="citations" /> 62 <expand macro="citations" />
59 </tool> 63 </tool>