Mercurial > repos > bgruening > diffbind
annotate diffbind.xml @ 3:d6dcb3dd5f8f draft
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 |
rev | line source |
---|---|
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
1 <tool id="diffbind" name="DiffBind" version="2.1.0"> |
0 | 2 <description> differential binding analysis of ChIP-Seq peak data</description> |
3 <requirements> | |
2
492d5ac7b2e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
1
diff
changeset
|
4 <requirement type="binary">Rscript</requirement> |
492d5ac7b2e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
1
diff
changeset
|
5 <requirement type="R-module">DESeq2</requirement> |
1 | 6 <requirement type="package" version="3.0.3">R</requirement> |
7 <requirement type="package" version="1.2.10">deseq2</requirement> | |
0 | 8 <requirement type="package" version="1.8.3">diffbind</requirement> |
9 </requirements> | |
10 <stdio> | |
1 | 11 <regex match="Execution halted" |
12 source="both" | |
13 level="fatal" | |
0 | 14 description="Execution halted." /> |
1 | 15 <regex match="Input-Error 01" |
16 source="both" | |
17 level="fatal" | |
0 | 18 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> |
1 | 19 <regex match="Error in" |
20 source="both" | |
21 level="fatal" | |
0 | 22 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
23 </stdio> | |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
24 <command> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
25 <![CDATA[ |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
26 ## seems that diffbind also needs file extensions to work properly |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
27 #set $counter = 1 |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
28 #for $sample in $samples: |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
29 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
30 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
31 #if str( $sample.bamcontrol ) != 'None': |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
32 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
33 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
34 #end if |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
35 #set $counter = $counter + 1 |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
36 #end for |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
37 |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
38 Rscript $__tool_directory__/diffbind.R |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
39 -i $infile |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
40 -o $outfile |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
41 -p $plots |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
42 -f $format |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
43 ]]> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
44 </command> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
45 <configfiles> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
46 <configfile name="infile"> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
47 #set $counter = 1 |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
48 #for $sample in $samples: |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
49 #if str( $sample.bamcontrol ) != 'None' and $counter == 1: |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
50 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
51 #elif $counter == 1: |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
52 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
53 #end if |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
54 #if str( $sample.bamcontrol ) != 'None': |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
55 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
56 #else: |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
58 #end if |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
59 #set $counter = $counter + 1 |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
60 #end for |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
61 </configfile> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
62 </configfiles> |
0 | 63 <inputs> |
64 <repeat name="samples" title="Samples" min="2"> | |
65 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> | |
66 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" /> | |
67 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" /> | |
68 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" /> | |
69 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" /> | |
70 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/> | |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
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."/> |
0 | 72 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> |
73 </repeat> | |
1 | 74 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" |
0 | 75 label="Visualising the analysis results" |
76 help="output an additional PDF files" /> | |
77 <param name="format" type="select" label="Output Format"> | |
78 <option value="bed">BED</option> | |
79 <option value="gff">GFF</option> | |
80 <option value="wig">WIG</option> | |
81 </param> | |
82 </inputs> | |
83 <outputs> | |
84 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> | |
85 <change_format> | |
86 <when input="format" value="wig" format="wig" /> | |
87 <when input="format" value="gff" format="gff" /> | |
88 </change_format> | |
89 </data> | |
90 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> | |
91 <filter>pdf == True</filter> | |
92 </data> | |
93 </outputs> | |
94 <help> | |
1 | 95 <![CDATA[ |
0 | 96 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
97 What it does |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
98 ************ |
0 | 99 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
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. |
1 | 101 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
102 Input |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
103 ***** |
1 | 104 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
105 * You have to specify your samples. Here is one example:: |
1 | 106 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
107 ID Tissue Factor Condition Treatment Replicate Caller Intervals |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
108 BT4741 BT474 ER Resistant Full-Media 1 raw 1084 |
0 | 109 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
110 * BAM file which contains the mapped sequencing reads can be associated with each peakset |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
111 * Control BAM file represents a control dataset and are optional, but have to specified for all when used. |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
112 * Peak file: Result of your Peak calling experiment |
1 | 113 |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
114 Output |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
115 ****** |
0 | 116 |
1 | 117 As output format you can choose BED, GFF, WIG. |
118 | |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
119 References |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
120 ********** |
1 | 121 |
122 DiffBind_ Authors: Rory Stark, Gordon Brown (2011) | |
0 | 123 |
124 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html | |
125 | |
126 Wrapper authors: Bjoern Gruening, Pavankumar Videm | |
127 | |
1 | 128 ]]> |
0 | 129 </help> |
3
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
130 <citations> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
131 <citation type="doi">doi:10.1038/nature10730</citation> |
d6dcb3dd5f8f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents:
2
diff
changeset
|
132 </citations> |
0 | 133 </tool> |