Mercurial > repos > bgruening > diffbind

comparison diffbind.xml @ 1:9e9f85c20d99 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 08 Sep 2015 05:38:45 -0400
parents 7faaf4a5e4e1
children 492d5ac7b2e2
comparison
equal deleted inserted replaced
0:7faaf4a5e4e1 1:9e9f85c20d99
1 <tool id="diffbind" name="DiffBind" version="2.0.1"> 1 <tool id="diffbind" name="DiffBind" version="2.0.2">
2 <description> differential binding analysis of ChIP-Seq peak data</description> 2 <description> differential binding analysis of ChIP-Seq peak data</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">Rscript</requirement> 4 <requirement type="package" version="3.0.3">R</requirement>
5 <requirement type="R-module">DESeq2</requirement> 5 <requirement type="package" version="1.2.10">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> 6 <requirement type="package" version="1.8.3">diffbind</requirement>
9 </requirements> 7 </requirements>
10 <command> 8 <command>
9 <![CDATA[
11 ## seems that diffbind also needs file extensions to work properly 10 ## seems that diffbind also needs file extensions to work properly
12 #set $counter = 1 11 #set $counter = 1
13 #for $sample in $samples: 12 #for $sample in $samples:
14 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &amp;&amp; 13 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
15 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp; 14 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
16 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp; 15 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
17 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp; 16 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
18 #set $counter = $counter + 1 17 #set $counter = $counter + 1
19 #end for 18 #end for
20 19
21 Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R 20 Rscript $__tool_directory__/diffbind.R
22 -i $infile 21 -i $infile
23 -o $outfile 22 -o $outfile
24 -p $plots 23 -p $plots
25 -f $format 24 -f $format
25 ]]>
26 </command> 26 </command>
27 <stdio> 27 <stdio>
28 <regex match="Execution halted" 28 <regex match="Execution halted"
29 source="both" 29 source="both"
30 level="fatal" 30 level="fatal"
31 description="Execution halted." /> 31 description="Execution halted." />
32 <regex match="Input-Error 01" 32 <regex match="Input-Error 01"
33 source="both" 33 source="both"
34 level="fatal" 34 level="fatal"
35 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> 35 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
36 <regex match="Error in" 36 <regex match="Error in"
37 source="both" 37 source="both"
38 level="fatal" 38 level="fatal"
39 description="An undefined error occured, please check your intput carefully and contact your administrator." /> 39 description="An undefined error occured, please check your intput carefully and contact your administrator." />
40 </stdio> 40 </stdio>
41 <inputs> 41 <inputs>
42 <repeat name="samples" title="Samples" min="2"> 42 <repeat name="samples" title="Samples" min="2">
43 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> 43 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
47 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" /> 47 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
48 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/> 48 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
49 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/> 49 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
50 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> 50 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
51 </repeat> 51 </repeat>
52 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 52 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
53 label="Visualising the analysis results" 53 label="Visualising the analysis results"
54 help="output an additional PDF files" /> 54 help="output an additional PDF files" />
55 <param name="format" type="select" label="Output Format"> 55 <param name="format" type="select" label="Output Format">
56 <option value="bed">BED</option> 56 <option value="bed">BED</option>
57 <option value="gff">GFF</option> 57 <option value="gff">GFF</option>
79 <filter>pdf == True</filter> 79 <filter>pdf == True</filter>
80 </data> 80 </data>
81 </outputs> 81 </outputs>
82 82
83 <help> 83 <help>
84 84 <![CDATA[
85 .. class:: infomark
86
87 **What it does**
88 85
89 86
90 ------ 87 **What it does**
91 88
92 **References** 89 Diffbind provides functions for processing ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets.
93 90
94 DiffBind_ Authors: Rory Stark, Gordon Brown 91 **Input**
92
93 - You have to specify your samples. Here is one example:
94
95 ID Tissue Factor Condition Treatment Replicate Caller Intervals
96 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
97
98 - BAM file which contains the mapped sequencing reads can be associated with each
99 peakset
100
101 - Control BAM file represents a control dataset
102
103 - Peak file: Result of your Peak calling experiment
104
105
106 **Output**
107
108 As output format you can choose BED, GFF, WIG.
109
110
111 **References**
112
113 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
95 114
96 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html 115 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
97 116
98 Wrapper authors: Bjoern Gruening, Pavankumar Videm 117 Wrapper authors: Bjoern Gruening, Pavankumar Videm
99 118
119 ]]>
100 </help> 120 </help>
101 </tool> 121 </tool>