Mercurial > repos > kpbioteam > chipeakanno_annopeaks

annotate chipeakanno_annopeaks.xml @ 11:8a91d82803a9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 1d355e9a8d667b026e22e5f8956f19199c5af880
author kpbioteam
date Sat, 23 Jun 2018 06:15:12 -0400
parents b1274d30071e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
1 <tool id="chipeakanno_annopeaks" name="chipeakanno_annopeaks" version="0.1.0">
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
2 <description>annotate peaks by annoGR object in the given range</description>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
3 <requirements>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
4 <requirement type="package" version="3.12.0">bioconductor-chippeakanno</requirement>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
5 <requirement type="package" version="2.99.0">bioconductor-ensdb.hsapiens.v75</requirement>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
6 <requirement type="package" version="1.38.3">bioconductor-rtracklayer</requirement>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
7 </requirements>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
10
b1274d30071e planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty
kpbioteam
parents: 9
diff changeset
9 Rscript ${__tool_directory__}/chipeakanno_annopeaks.R "$input1" "$input2" "$input3" "$input4" "$input5" "$output1"
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
10 ]]></command>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
11 <inputs>
11
8a91d82803a9 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 1d355e9a8d667b026e22e5f8956f19199c5af880
kpbioteam
parents: 10
diff changeset
12 <param type="data" name="input1" format="bedgraph" label="Differentially Methylated Data"/>
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
13 <param name="input2" type="select" label="bindingType" help="Specifying the criteria to associate peaks with annotation e.g. startSite start position of the feature strand">
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
14 <option value="startSite">startSite</option>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
15 <option value="endSite">endSite</option>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
16 <option value="fullRange">fullRange</option>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
17 <option value="nearestBiDirectionalPromoters">nearestBiDirectionalPromoters</option>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
18 </param>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
19 <param name="input3" type="text" value="-5000" label="bindingRegionStart" help="e.g. to obtain peaks within 5kb upstream and up to 3kb downstream of TSS within the gene body, set bindingType = startSite and bindingRegion = c(-5000, 3000)"/>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
20 <param name="input4" type="text" value="3000" label="bindingRegionEnd" help="e.g. to obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = nearestBiDirectionalPromoters and bindingRegion = c(-5000, 3000)"/>
9
8d05c398fecd planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty
kpbioteam
parents: 6
diff changeset
21
8d05c398fecd planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty
kpbioteam
parents: 6
diff changeset
22 <param name="input5" type="text" value="1" label="Additional Column of Score" help="Position of Additional Column of the Score" />
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
23 </inputs>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
24 <outputs>
11
8a91d82803a9 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 1d355e9a8d667b026e22e5f8956f19199c5af880
kpbioteam
parents: 10
diff changeset
25 <data name="output1" format="txt" label="Table of Annotated Peaks"/>
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
26 </outputs>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
27 <tests>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
28 <test>
6
ed66a80e81e8 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty
kpbioteam
parents: 5
diff changeset
29 <param name="input1" value="dmr.bedgraph"/>
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
30 <param name="input2" value="startSite"/>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
31 <param name="input3" value="-5000"/>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
32 <param name="input4" value="5000"/>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
33 <output name="output1" file="annoTab.txt"/>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
34 </test>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
35 </tests>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
36 <help><![CDATA[
2
ad60ed89de63 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5b7c2e824bb5cc85bf8711eca1cc94c68998ebb2-dirty
kpbioteam
parents: 1
diff changeset
37 This tool annotate peaks from bed file.
0
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
38 bindingType
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
39 Specifying the criteria to associate peaks with annotation. Here is how to use it together with the parameter bindingRegion
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
40 To obtain peaks within 5kb upstream and up to 3kb downstream of TSS within the gene body, set bindingType = "startSite" and bindingRegion = c(-5000, 3000)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
41 To obtain peaks up to 5kb upstream within the gene body and 3kb downstream of gene/Exon End, set bindingType = "endSite" and bindingRegion = c(-5000, 3000)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
42 To obtain peaks from 5kb upstream to 3kb downstream of genes/Exons , set bindingType = "fullRange" and bindingRegion = c(-5000, 3000)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
43 To obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = "nearestBiDirectionalPromoters" and bindingRegion = c(-5000, 3000)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
44 startSite
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
45 start position of the feature (strand is considered)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
46 endSite
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
47 end position of the feature (strand is considered)
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
48 fullRange
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
49 whole range of the feature
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
50 nearestBiDirectionalPromoters
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
51 nearest promoters from both direction of the peaks (strand is considered). It will report bidirectional promoters if there are promoters in both directions in the given region (defined by bindingRegion). Otherwise, it will report the closest promoter in one direction.
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
52 bindingRegion
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
53 Annotation range used together with bindingType, which is a vector with two integer values, default to c (-5000, 5000). The first one must be no bigger than 0. And the sec ond one must be no less than 1. For details, see bindingType.
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
54 ignore.peak.strand
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
55 ignore the peaks strand or not.
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
56 ]]></help>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
57 <citations>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
58 <citation type="doi">10.18129/B9.bioc.ChIPpeakAnno</citation>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
59 </citations>
efd9e1315ed5 planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
kpbioteam
parents:
diff changeset
60 </tool>