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comparison diffbind.xml @ 3:d6dcb3dd5f8f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
author bgruening
date Tue, 08 Mar 2016 08:13:00 -0500
parents 492d5ac7b2e2
children 69138bfd8644
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2:492d5ac7b2e2 3:d6dcb3dd5f8f
1 <tool id="diffbind" name="DiffBind" version="2.0.2"> 1 <tool id="diffbind" name="DiffBind" version="2.1.0">
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="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 </requirements> 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> 10 <stdio>
30 <regex match="Execution halted" 11 <regex match="Execution halted"
31 source="both" 12 source="both"
32 level="fatal" 13 level="fatal"
33 description="Execution halted." /> 14 description="Execution halted." />
38 <regex match="Error in" 19 <regex match="Error in"
39 source="both" 20 source="both"
40 level="fatal" 21 level="fatal"
41 description="An undefined error occured, please check your intput carefully and contact your administrator." /> 22 description="An undefined error occured, please check your intput carefully and contact your administrator." />
42 </stdio> 23 </stdio>
24 <command>
25 <![CDATA[
26 ## seems that diffbind also needs file extensions to work properly
27 #set $counter = 1
28 #for $sample in $samples:
29 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
30 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
31 #if str( $sample.bamcontrol ) != 'None':
32 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
33 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
34 #end if
35 #set $counter = $counter + 1
36 #end for
37
38 Rscript $__tool_directory__/diffbind.R
39 -i $infile
40 -o $outfile
41 -p $plots
42 -f $format
43 ]]>
44 </command>
45 <configfiles>
46 <configfile name="infile">
47 #set $counter = 1
48 #for $sample in $samples:
49 #if str( $sample.bamcontrol ) != 'None' and $counter == 1:
50 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
51 #elif $counter == 1:
52 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks
53 #end if
54 #if str( $sample.bamcontrol ) != 'None':
55 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
56 #else:
57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks
58 #end if
59 #set $counter = $counter + 1
60 #end for
61 </configfile>
62 </configfiles>
43 <inputs> 63 <inputs>
44 <repeat name="samples" title="Samples" min="2"> 64 <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-" /> 65 <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" /> 66 <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" /> 67 <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" /> 68 <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" /> 69 <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."/> 70 <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."/> 71 <param format="bam" name="bamcontrol" type="data" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/>
52 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> 72 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
53 </repeat> 73 </repeat>
54 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 74 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
55 label="Visualising the analysis results" 75 label="Visualising the analysis results"
56 help="output an additional PDF files" /> 76 help="output an additional PDF files" />
58 <option value="bed">BED</option> 78 <option value="bed">BED</option>
59 <option value="gff">GFF</option> 79 <option value="gff">GFF</option>
60 <option value="wig">WIG</option> 80 <option value="wig">WIG</option>
61 </param> 81 </param>
62 </inputs> 82 </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> 83 <outputs>
74 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> 84 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
75 <change_format> 85 <change_format>
76 <when input="format" value="wig" format="wig" /> 86 <when input="format" value="wig" format="wig" />
77 <when input="format" value="gff" format="gff" /> 87 <when input="format" value="gff" format="gff" />
79 </data> 89 </data>
80 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> 90 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
81 <filter>pdf == True</filter> 91 <filter>pdf == True</filter>
82 </data> 92 </data>
83 </outputs> 93 </outputs>
84
85 <help> 94 <help>
86 <![CDATA[ 95 <![CDATA[
87 96
97 What it does
98 ************
88 99
89 **What it does** 100 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.
90 101
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. 102 Input
103 *****
92 104
93 **Input** 105 * You have to specify your samples. Here is one example::
94 106
95 - You have to specify your samples. Here is one example: 107 ID Tissue Factor Condition Treatment Replicate Caller Intervals
108 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
96 109
97 ID Tissue Factor Condition Treatment Replicate Caller Intervals 110 * BAM file which contains the mapped sequencing reads can be associated with each peakset
98 BT4741 BT474 ER Resistant Full-Media 1 raw 1084 111 * Control BAM file represents a control dataset and are optional, but have to specified for all when used.
112 * Peak file: Result of your Peak calling experiment
99 113
100 - BAM file which contains the mapped sequencing reads can be associated with each 114 Output
101 peakset 115 ******
102
103 - Control BAM file represents a control dataset
104
105 - Peak file: Result of your Peak calling experiment
106
107
108 **Output**
109 116
110 As output format you can choose BED, GFF, WIG. 117 As output format you can choose BED, GFF, WIG.
111 118
112 119 References
113 **References** 120 **********
114 121
115 DiffBind_ Authors: Rory Stark, Gordon Brown (2011) 122 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
116 123
117 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html 124 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
118 125
119 Wrapper authors: Bjoern Gruening, Pavankumar Videm 126 Wrapper authors: Bjoern Gruening, Pavankumar Videm
120 127
121 ]]> 128 ]]>
122 </help> 129 </help>
130 <citations>
131 <citation type="doi">doi:10.1038/nature10730</citation>
132 </citations>
123 </tool> 133 </tool>