|
1
|
1 <tool id="diffbind" name="DiffBind" version="2.0.3">
|
|
0
|
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>
|
|
1
|
6 <requirement type="package" version="3.1.0">R</requirement>
|
|
0
|
7 <requirement type="package" version="1.2.10">deseq2</requirement>
|
|
1
|
8 <requirement type="package" version="1.14.4">diffbind</requirement>
|
|
0
|
9 </requirements>
|
|
|
10 <command>
|
|
|
11 <![CDATA[
|
|
|
12 ## seems that diffbind also needs file extensions to work properly
|
|
|
13 #set $counter = 1
|
|
|
14 #for $sample in $samples:
|
|
|
15 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
|
|
|
16 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
|
|
|
17 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
|
|
|
18 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
|
|
|
19 #set $counter = $counter + 1
|
|
|
20 #end for
|
|
|
21
|
|
|
22 Rscript $__tool_directory__/diffbind.R
|
|
|
23 -i $infile
|
|
|
24 -o $outfile
|
|
|
25 -p $plots
|
|
|
26 -f $format
|
|
|
27 ]]>
|
|
|
28 </command>
|
|
|
29 <stdio>
|
|
|
30 <regex match="Execution halted"
|
|
|
31 source="both"
|
|
|
32 level="fatal"
|
|
|
33 description="Execution halted." />
|
|
|
34 <regex match="Input-Error 01"
|
|
|
35 source="both"
|
|
|
36 level="fatal"
|
|
|
37 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
|
|
|
38 <regex match="Error in"
|
|
|
39 source="both"
|
|
|
40 level="fatal"
|
|
|
41 description="An undefined error occured, please check your intput carefully and contact your administrator." />
|
|
|
42 </stdio>
|
|
|
43 <inputs>
|
|
|
44 <repeat name="samples" title="Samples" min="2">
|
|
|
45 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
|
|
|
46 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
|
|
|
47 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
|
|
|
48 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
|
|
|
49 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
|
|
|
50 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
|
|
|
51 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
|
|
|
52 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
|
|
|
53 </repeat>
|
|
|
54 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
|
|
|
55 label="Visualising the analysis results"
|
|
|
56 help="output an additional PDF files" />
|
|
|
57 <param name="format" type="select" label="Output Format">
|
|
|
58 <option value="bed">BED</option>
|
|
|
59 <option value="gff">GFF</option>
|
|
|
60 <option value="wig">WIG</option>
|
|
|
61 </param>
|
|
|
62 </inputs>
|
|
|
63 <configfiles>
|
|
|
64 <configfile name="infile">
|
|
|
65 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
|
|
|
66 #set $counter = 1
|
|
|
67 #for $sample in $samples:
|
|
|
68 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
|
|
|
69 #set $counter = $counter + 1
|
|
|
70 #end for
|
|
|
71 </configfile>
|
|
|
72 </configfiles>
|
|
|
73 <outputs>
|
|
|
74 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
|
|
|
75 <change_format>
|
|
|
76 <when input="format" value="wig" format="wig" />
|
|
|
77 <when input="format" value="gff" format="gff" />
|
|
|
78 </change_format>
|
|
|
79 </data>
|
|
|
80 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
|
|
|
81 <filter>pdf == True</filter>
|
|
|
82 </data>
|
|
|
83 </outputs>
|
|
|
84
|
|
|
85 <help>
|
|
|
86 <![CDATA[
|
|
|
87
|
|
|
88 .. class:: infomark
|
|
|
89
|
|
|
90 **What it does**
|
|
|
91
|
|
|
92
|
|
|
93 ------
|
|
|
94
|
|
|
95 **References**
|
|
|
96
|
|
|
97 DiffBind_ Authors: Rory Stark, Gordon Brown
|
|
|
98
|
|
|
99 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
|
|
|
100
|
|
|
101 Wrapper authors: Bjoern Gruening, Pavankumar Videm
|
|
|
102
|
|
|
103 ]]>
|
|
|
104 </help>
|
|
|
105 </tool>
|
