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initial commit for DiffBind
author bjoern-gruening
date Tue, 14 Jan 2014 18:12:02 -0500
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-1:000000000000 0:c0f5b2133506
1 <tool id="diffbind" name="DiffBind" version="2.0.1">
2 <description> differential binding analysis of ChIP-Seq peak data</description>
3 <requirements>
4 <requirement type="binary">Rscript</requirement>
5 <requirement type="R-module">DESeq2</requirement>
6 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
7 <requirement type="package" version="1.0.17">deseq2</requirement>
8 <requirement type="package" version="1.8.3">diffbind</requirement>
9 </requirements>
10 <command interpreter="Rscript">
11 diffbind.R
12 -i $infile
13 -o $outfile
14 -p $plots
15 -f $format
16 ;
17 cat $infile;
18 </command>
19 <stdio>
20 <regex match="Execution halted"
21 source="both"
22 level="fatal"
23 description="Execution halted." />
24 <regex match="Input-Error 01"
25 source="both"
26 level="fatal"
27 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
28 <regex match="Error in"
29 source="both"
30 level="fatal"
31 description="An undefined error occured, please check your intput carefully and contact your administrator." />
32 </stdio>
33 <inputs>
34 <repeat name="samples" title="Samples" min="2">
35 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
36 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
37 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
38 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
39 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
40 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
41 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
42 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
43 </repeat>
44 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
45 label="Visualising the analysis results"
46 help="output an additional PDF files" />
47 <param name="format" type="select" label="Output Format">
48 <option value="bed">BED</option>
49 <option value="gff">GFF</option>
50 <option value="wig">WIG</option>
51 </param>
52 </inputs>
53 <configfiles>
54 <configfile name="infile">
55 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
56 #for $sample in $samples:
57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks
58 #end for
59 </configfile>
60 </configfiles>
61 <outputs>
62 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
63 <change_format>
64 <when input="format" value="wig" format="wig" />
65 <when input="format" value="gff" format="gff" />
66 </change_format>
67 </data>
68 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
69 <filter>pdf == True</filter>
70 </data>
71 </outputs>
72
73 <help>
74
75 .. class:: infomark
76
77 **What it does**
78
79
80 ------
81
82 **References**
83
84 DiffBind_ Authors: Rory Stark, Gordon Brown
85
86 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
87
88 Wrapper authors: Bjoern Gruening, Pavankumar Videm
89
90 </help>
91 </tool>