Mercurial > repos > bgruening > diffbind
annotate diffbind.xml @ 2:492d5ac7b2e2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
| author | bgruening |
|---|---|
| date | Fri, 26 Feb 2016 13:36:05 -0500 |
| parents | 9e9f85c20d99 |
| children | d6dcb3dd5f8f |
| rev | line source |
|---|---|
| 1 | 1 <tool id="diffbind" name="DiffBind" version="2.0.2"> |
| 0 | 2 <description> differential binding analysis of ChIP-Seq peak data</description> |
| 3 <requirements> | |
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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 <command> | |
| 1 | 11 <![CDATA[ |
| 0 | 12 ## seems that diffbind also needs file extensions to work properly |
| 13 #set $counter = 1 | |
| 14 #for $sample in $samples: | |
| 1 | 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"# && | |
| 0 | 19 #set $counter = $counter + 1 |
| 20 #end for | |
| 21 | |
| 1 | 22 Rscript $__tool_directory__/diffbind.R |
| 0 | 23 -i $infile |
| 24 -o $outfile | |
| 25 -p $plots | |
| 26 -f $format | |
| 1 | 27 ]]> |
| 0 | 28 </command> |
| 29 <stdio> | |
| 1 | 30 <regex match="Execution halted" |
| 31 source="both" | |
| 32 level="fatal" | |
| 0 | 33 description="Execution halted." /> |
| 1 | 34 <regex match="Input-Error 01" |
| 35 source="both" | |
| 36 level="fatal" | |
| 0 | 37 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> |
| 1 | 38 <regex match="Error in" |
| 39 source="both" | |
| 40 level="fatal" | |
| 0 | 41 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
| 42 </stdio> | |
| 43 <inputs> | |
| 44 <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-" /> | |
| 46 <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" /> | |
| 48 <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" /> | |
| 50 <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."/> | |
| 52 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> | |
| 53 </repeat> | |
| 1 | 54 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" |
| 0 | 55 label="Visualising the analysis results" |
| 56 help="output an additional PDF files" /> | |
| 57 <param name="format" type="select" label="Output Format"> | |
| 58 <option value="bed">BED</option> | |
| 59 <option value="gff">GFF</option> | |
| 60 <option value="wig">WIG</option> | |
| 61 </param> | |
| 62 </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> | |
| 74 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> | |
| 75 <change_format> | |
| 76 <when input="format" value="wig" format="wig" /> | |
| 77 <when input="format" value="gff" format="gff" /> | |
| 78 </change_format> | |
| 79 </data> | |
| 80 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> | |
| 81 <filter>pdf == True</filter> | |
| 82 </data> | |
| 83 </outputs> | |
| 84 | |
| 85 <help> | |
| 1 | 86 <![CDATA[ |
| 0 | 87 |
| 88 | |
| 1 | 89 **What it does** |
| 90 | |
| 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. | |
| 92 | |
| 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 | |
| 0 | 102 |
| 1 | 103 - Control BAM file represents a control dataset |
| 104 | |
| 105 - Peak file: Result of your Peak calling experiment | |
| 106 | |
| 107 | |
| 108 **Output** | |
| 0 | 109 |
| 1 | 110 As output format you can choose BED, GFF, WIG. |
| 111 | |
| 112 | |
| 113 **References** | |
| 114 | |
| 115 DiffBind_ Authors: Rory Stark, Gordon Brown (2011) | |
| 0 | 116 |
| 117 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html | |
| 118 | |
| 119 Wrapper authors: Bjoern Gruening, Pavankumar Videm | |
| 120 | |
| 1 | 121 ]]> |
| 0 | 122 </help> |
| 123 </tool> |