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comparison diffbind.xml @ 15:aefe2a771a95 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
author bgruening
date Fri, 26 Feb 2016 13:35:28 -0500
parents 4de6355eca00
children 128584543be7
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14:4de6355eca00 15:aefe2a771a95
4 <requirement type="binary">Rscript</requirement> 4 <requirement type="binary">Rscript</requirement>
5 <requirement type="R-module">DESeq2</requirement> 5 <requirement type="R-module">DESeq2</requirement>
6 <requirement type="package" version="3.0.3">R</requirement> 6 <requirement type="package" version="3.0.3">R</requirement>
7 <requirement type="package" version="1.2.10">deseq2</requirement> 7 <requirement type="package" version="1.2.10">deseq2</requirement>
8 <requirement type="package" version="1.8.3">diffbind</requirement> 8 <requirement type="package" version="1.8.3">diffbind</requirement>
9 <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</requirement>
10 </requirements> 9 </requirements>
11 <command> 10 <command>
11 <![CDATA[
12 ## seems that diffbind also needs file extensions to work properly 12 ## seems that diffbind also needs file extensions to work properly
13 #set $counter = 1 13 #set $counter = 1
14 #for $sample in $samples: 14 #for $sample in $samples:
15 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &amp;&amp; 15 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
16 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp; 16 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
17 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp; 17 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
18 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp; 18 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
19 #set $counter = $counter + 1 19 #set $counter = $counter + 1
20 #end for 20 #end for
21 21
22 Rscript \$DIFFBIND_SCRIPT_PATH/diffbind.R 22 Rscript $__tool_directory__/diffbind.R
23 -i $infile 23 -i $infile
24 -o $outfile 24 -o $outfile
25 -p $plots 25 -p $plots
26 -f $format 26 -f $format
27 ]]>
27 </command> 28 </command>
28 <stdio> 29 <stdio>
29 <regex match="Execution halted" 30 <regex match="Execution halted"
30 source="both" 31 source="both"
31 level="fatal" 32 level="fatal"
32 description="Execution halted." /> 33 description="Execution halted." />
33 <regex match="Input-Error 01" 34 <regex match="Input-Error 01"
34 source="both" 35 source="both"
35 level="fatal" 36 level="fatal"
36 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> 37 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
37 <regex match="Error in" 38 <regex match="Error in"
38 source="both" 39 source="both"
39 level="fatal" 40 level="fatal"
40 description="An undefined error occured, please check your intput carefully and contact your administrator." /> 41 description="An undefined error occured, please check your intput carefully and contact your administrator." />
41 </stdio> 42 </stdio>
42 <inputs> 43 <inputs>
43 <repeat name="samples" title="Samples" min="2"> 44 <repeat name="samples" title="Samples" min="2">
44 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> 45 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
48 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" /> 49 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
49 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/> 50 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
50 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control 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."/>
51 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> 52 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
52 </repeat> 53 </repeat>
53 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 54 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
54 label="Visualising the analysis results" 55 label="Visualising the analysis results"
55 help="output an additional PDF files" /> 56 help="output an additional PDF files" />
56 <param name="format" type="select" label="Output Format"> 57 <param name="format" type="select" label="Output Format">
57 <option value="bed">BED</option> 58 <option value="bed">BED</option>
58 <option value="gff">GFF</option> 59 <option value="gff">GFF</option>
80 <filter>pdf == True</filter> 81 <filter>pdf == True</filter>
81 </data> 82 </data>
82 </outputs> 83 </outputs>
83 84
84 <help> 85 <help>
85 86 <![CDATA[
86 .. class:: infomark
87
88 **What it does**
89 87
90 88
91 ------ 89 **What it does**
92 90
93 **References** 91 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.
94 92
95 DiffBind_ Authors: Rory Stark, Gordon Brown 93 **Input**
94
95 - You have to specify your samples. Here is one example:
96
97 ID Tissue Factor Condition Treatment Replicate Caller Intervals
98 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
99
100 - BAM file which contains the mapped sequencing reads can be associated with each
101 peakset
102
103 - Control BAM file represents a control dataset
104
105 - Peak file: Result of your Peak calling experiment
106
107
108 **Output**
109
110 As output format you can choose BED, GFF, WIG.
111
112
113 **References**
114
115 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
96 116
97 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html 117 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
98 118
99 Wrapper authors: Bjoern Gruening, Pavankumar Videm 119 Wrapper authors: Bjoern Gruening, Pavankumar Videm
100 120
121 ]]>
101 </help> 122 </help>
102 </tool> 123 </tool>