Mercurial > repos > bgruening > diffbind

annotate diffbind.xml @ 19:ab544462062a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
author bgruening
date Sat, 28 Oct 2017 12:55:12 -0400
parents 33474c277ba0
children 11cd8b1ae397
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
ab544462062a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
bgruening
parents: 18
diff changeset
1 <tool id="diffbind" name="DiffBind" version="2.2.2">
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
2 <description> differential binding analysis of ChIP-Seq peak data</description>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
3 <requirements>
18
33474c277ba0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n'
bgruening
parents: 17
diff changeset
4 <requirement type="package" version="2.0.9">bioconductor-diffbind</requirement>
19
ab544462062a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
bgruening
parents: 18
diff changeset
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
6 </requirements>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
7 <stdio>
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
8 <regex match="Execution halted"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
9 source="both"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
10 level="fatal"
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
11 description="Execution halted." />
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
12 <regex match="Input-Error 01"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
13 source="both"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
14 level="fatal"
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
15 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
16 <regex match="Error in"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
17 source="both"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
18 level="fatal"
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
19 description="An undefined error occured, please check your intput carefully and contact your administrator." />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
20 </stdio>
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
21 <command>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
22 <![CDATA[
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
23 ## seems that diffbind also needs file extensions to work properly
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
24 #set $counter = 1
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
25 #for $sample in $samples:
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
26 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
27 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
28 #if str( $sample.bamcontrol ) != 'None':
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
29 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
30 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
31 #end if
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
32 #set $counter = $counter + 1
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
33 #end for
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
34
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
35 Rscript $__tool_directory__/diffbind.R
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
36 -i $infile
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
37 -o $outfile
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
38 -p $plots
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
39 -f $format
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
40 ]]>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
41 </command>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
42 <configfiles>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
43 <configfile name="infile">
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
44 #set $counter = 1
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
45 #for $sample in $samples:
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
46 #if str( $sample.bamcontrol ) != 'None' and $counter == 1:
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
47 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
48 #elif $counter == 1:
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
49 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
50 #end if
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
51 #if str( $sample.bamcontrol ) != 'None':
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
52 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
53 #else:
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
54 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
55 #end if
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
56 #set $counter = $counter + 1
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
57 #end for
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
58 </configfile>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
59 </configfiles>
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
60 <inputs>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
61 <repeat name="samples" title="Samples" min="2">
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
62 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
63 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
64 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
65 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
3
4f2b7248886c Uploaded
bgruening
parents: 2
diff changeset
66 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
67 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
68 <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."/>
4
aad86ce28779 Uploaded
bgruening
parents: 3
diff changeset
69 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
70 </repeat>
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
71 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
72 label="Visualising the analysis results"
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
73 help="output an additional PDF files" />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
74 <param name="format" type="select" label="Output Format">
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
75 <option value="bed">BED</option>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
76 <option value="gff">GFF</option>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
77 <option value="wig">WIG</option>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
78 </param>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
79 </inputs>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
80 <outputs>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
81 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
82 <change_format>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
83 <when input="format" value="wig" format="wig" />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
84 <when input="format" value="gff" format="gff" />
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
85 </change_format>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
86 </data>
9
20c431b4cf74 Uploaded
bgruening
parents: 6
diff changeset
87 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
88 <filter>pdf == True</filter>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
89 </data>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
90 </outputs>
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
91 <help>
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
92 <![CDATA[
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
93
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
94 What it does
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
95 ************
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
96
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
97 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.
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
98
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
99 Input
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
100 *****
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
101
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
102 * You have to specify your samples. Here is one example::
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
103
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
104 ID Tissue Factor Condition Treatment Replicate Caller Intervals
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
105 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
106
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
107 * BAM file which contains the mapped sequencing reads can be associated with each peakset
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
108 * Control BAM file represents a control dataset and are optional, but have to specified for all when used.
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
109 * Peak file: Result of your Peak calling experiment
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
110
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
111 Output
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
112 ******
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
113
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
114 As output format you can choose BED, GFF, WIG.
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
115
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
116 References
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
117 **********
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
118
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
119 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
120
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
121 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
122
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
123 Wrapper authors: Bjoern Gruening, Pavankumar Videm
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
124
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 14
diff changeset
125 ]]>
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
126 </help>
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
127 <citations>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
128 <citation type="doi">doi:10.1038/nature10730</citation>
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
parents: 15
diff changeset
129 </citations>
0
8d48d5591389 Uploaded
bgruening
parents:
diff changeset
130 </tool>