diffbind: diffbind.xml annotate

annotate diffbind.xml @ 15:aefe2a771a95 draft

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

rev	line source
14 4de6355eca00 Uploaded bgruening parents: 12 diff changeset	1 <tool id="diffbind" name="DiffBind" version="2.0.2">
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>
8d48d5591389 Uploaded bgruening parents: diff changeset	4 <requirement type="binary">Rscript</requirement>
8d48d5591389 Uploaded bgruening parents: diff changeset	5 <requirement type="R-module">DESeq2</requirement>
14 4de6355eca00 Uploaded bgruening parents: 12 diff changeset	6 <requirement type="package" version="3.0.3">R</requirement>
4de6355eca00 Uploaded bgruening parents: 12 diff changeset	7 <requirement type="package" version="1.2.10">deseq2</requirement>
6 da65ae70e2e1 Uploaded bgruening parents: 4 diff changeset	8 <requirement type="package" version="1.8.3">diffbind</requirement>
0 8d48d5591389 Uploaded bgruening parents: diff changeset	9 </requirements>
10 b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	10 <command>
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	11 <![CDATA[
10 b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	12 ## seems that diffbind also needs file extensions to work properly
b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	13 #set $counter = 1
b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	14 #for $sample in $samples:
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	15 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	16 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	17 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	18 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
10 b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	19 #set $counter = $counter + 1
b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	20 #end for
b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	21
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	22 Rscript $__tool_directory__/diffbind.R
0 8d48d5591389 Uploaded bgruening parents: diff changeset	23 -i $infile
8d48d5591389 Uploaded bgruening parents: diff changeset	24 -o $outfile
8d48d5591389 Uploaded bgruening parents: diff changeset	25 -p $plots
8d48d5591389 Uploaded bgruening parents: diff changeset	26 -f $format
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	27 ]]>
0 8d48d5591389 Uploaded bgruening parents: diff changeset	28 </command>
8d48d5591389 Uploaded bgruening parents: diff changeset	29 <stdio>
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	30 <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	31 source="both"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	32 level="fatal"
0 8d48d5591389 Uploaded bgruening parents: diff changeset	33 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	34 <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	35 source="both"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	36 level="fatal"
0 8d48d5591389 Uploaded bgruening parents: diff changeset	37 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	38 <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	39 source="both"
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	40 level="fatal"
0 8d48d5591389 Uploaded bgruening parents: diff changeset	41 description="An undefined error occured, please check your intput carefully and contact your administrator." />
8d48d5591389 Uploaded bgruening parents: diff changeset	42 </stdio>
8d48d5591389 Uploaded bgruening parents: diff changeset	43 <inputs>
8d48d5591389 Uploaded bgruening parents: diff changeset	44 <repeat name="samples" title="Samples" min="2">
8d48d5591389 Uploaded bgruening parents: diff changeset	45 <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	46 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
8d48d5591389 Uploaded bgruening parents: diff changeset	47 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
8d48d5591389 Uploaded bgruening parents: diff changeset	48 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
3 4f2b7248886c Uploaded bgruening parents: 2 diff changeset	49 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
0 8d48d5591389 Uploaded bgruening parents: diff changeset	50 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
8d48d5591389 Uploaded bgruening parents: diff changeset	51 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
4 aad86ce28779 Uploaded bgruening parents: 3 diff changeset	52 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
0 8d48d5591389 Uploaded bgruening parents: diff changeset	53 </repeat>
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	54 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
0 8d48d5591389 Uploaded bgruening parents: diff changeset	55 label="Visualising the analysis results"
8d48d5591389 Uploaded bgruening parents: diff changeset	56 help="output an additional PDF files" />
8d48d5591389 Uploaded bgruening parents: diff changeset	57 <param name="format" type="select" label="Output Format">
8d48d5591389 Uploaded bgruening parents: diff changeset	58 <option value="bed">BED</option>
8d48d5591389 Uploaded bgruening parents: diff changeset	59 <option value="gff">GFF</option>
8d48d5591389 Uploaded bgruening parents: diff changeset	60 <option value="wig">WIG</option>
8d48d5591389 Uploaded bgruening parents: diff changeset	61 </param>
8d48d5591389 Uploaded bgruening parents: diff changeset	62 </inputs>
8d48d5591389 Uploaded bgruening parents: diff changeset	63 <configfiles>
9 20c431b4cf74 Uploaded bgruening parents: 6 diff changeset	64 <configfile name="infile">
0 8d48d5591389 Uploaded bgruening parents: diff changeset	65 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
10 b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	66 #set $counter = 1
0 8d48d5591389 Uploaded bgruening parents: diff changeset	67 #for $sample in $samples:
10 b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	68 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
b1b96b6ed60c Uploaded bgruening parents: 9 diff changeset	69 #set $counter = $counter + 1
0 8d48d5591389 Uploaded bgruening parents: diff changeset	70 #end for
9 20c431b4cf74 Uploaded bgruening parents: 6 diff changeset	71 </configfile>
0 8d48d5591389 Uploaded bgruening parents: diff changeset	72 </configfiles>
8d48d5591389 Uploaded bgruening parents: diff changeset	73 <outputs>
8d48d5591389 Uploaded bgruening parents: diff changeset	74 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
8d48d5591389 Uploaded bgruening parents: diff changeset	75 <change_format>
8d48d5591389 Uploaded bgruening parents: diff changeset	76 <when input="format" value="wig" format="wig" />
8d48d5591389 Uploaded bgruening parents: diff changeset	77 <when input="format" value="gff" format="gff" />
8d48d5591389 Uploaded bgruening parents: diff changeset	78 </change_format>
8d48d5591389 Uploaded bgruening parents: diff changeset	79 </data>
9 20c431b4cf74 Uploaded bgruening parents: 6 diff changeset	80 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
0 8d48d5591389 Uploaded bgruening parents: diff changeset	81 <filter>pdf == True</filter>
8d48d5591389 Uploaded bgruening parents: diff changeset	82 </data>
8d48d5591389 Uploaded bgruening parents: diff changeset	83 </outputs>
8d48d5591389 Uploaded bgruening parents: diff changeset	84
8d48d5591389 Uploaded bgruening parents: diff changeset	85 <help>
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	86 <![CDATA[
0 8d48d5591389 Uploaded bgruening parents: diff changeset	87
8d48d5591389 Uploaded bgruening parents: diff changeset	88
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	89 What it does
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	90
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	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.
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	92
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	93 Input
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	94
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	95 - You have to specify your samples. Here is one example:
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	96
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	97 ID Tissue Factor Condition Treatment Replicate Caller Intervals
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	98 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	99
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	100 - BAM file which contains the mapped sequencing reads can be associated with each
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	101 peakset
0 8d48d5591389 Uploaded bgruening parents: diff changeset	102
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	103 - Control BAM file represents a control dataset
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	104
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	105 - Peak file: Result of your Peak calling experiment
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	106
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	107
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	108 Output
0 8d48d5591389 Uploaded bgruening parents: diff changeset	109
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	110 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	111
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	112
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	113 References
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	114
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	115 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
0 8d48d5591389 Uploaded bgruening parents: diff changeset	116
8d48d5591389 Uploaded bgruening parents: diff changeset	117 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
8d48d5591389 Uploaded bgruening parents: diff changeset	118
8d48d5591389 Uploaded bgruening parents: diff changeset	119 Wrapper authors: Bjoern Gruening, Pavankumar Videm
8d48d5591389 Uploaded bgruening parents: diff changeset	120
15 aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 14 diff changeset	121 ]]>
0 8d48d5591389 Uploaded bgruening parents: diff changeset	122 </help>
8d48d5591389 Uploaded bgruening parents: diff changeset	123 </tool>

Mercurial > repos > bgruening > diffbind

annotate diffbind.xml @ 15:aefe2a771a95 draft