Mercurial > repos > bgruening > diffbind
comparison diffbind.xml @ 0:7faaf4a5e4e1 draft
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| author | bgruening |
|---|---|
| date | Thu, 16 Jan 2014 04:15:09 -0500 |
| parents | |
| children | 9e9f85c20d99 |
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| -1:000000000000 | 0:7faaf4a5e4e1 |
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| 1 <tool id="diffbind" name="DiffBind" version="2.0.1"> | |
| 2 <description> differential binding analysis of ChIP-Seq peak data</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">Rscript</requirement> | |
| 5 <requirement type="R-module">DESeq2</requirement> | |
| 6 <requirement type="package" version="3.0.1">R_3_0_1</requirement> | |
| 7 <requirement type="package" version="1.0.17">deseq2</requirement> | |
| 8 <requirement type="package" version="1.8.3">diffbind</requirement> | |
| 9 </requirements> | |
| 10 <command> | |
| 11 ## seems that diffbind also needs file extensions to work properly | |
| 12 #set $counter = 1 | |
| 13 #for $sample in $samples: | |
| 14 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && | |
| 15 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && | |
| 16 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && | |
| 17 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && | |
| 18 #set $counter = $counter + 1 | |
| 19 #end for | |
| 20 | |
| 21 Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R | |
| 22 -i $infile | |
| 23 -o $outfile | |
| 24 -p $plots | |
| 25 -f $format | |
| 26 </command> | |
| 27 <stdio> | |
| 28 <regex match="Execution halted" | |
| 29 source="both" | |
| 30 level="fatal" | |
| 31 description="Execution halted." /> | |
| 32 <regex match="Input-Error 01" | |
| 33 source="both" | |
| 34 level="fatal" | |
| 35 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> | |
| 36 <regex match="Error in" | |
| 37 source="both" | |
| 38 level="fatal" | |
| 39 description="An undefined error occured, please check your intput carefully and contact your administrator." /> | |
| 40 </stdio> | |
| 41 <inputs> | |
| 42 <repeat name="samples" title="Samples" min="2"> | |
| 43 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> | |
| 44 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" /> | |
| 45 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" /> | |
| 46 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" /> | |
| 47 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" /> | |
| 48 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/> | |
| 49 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/> | |
| 50 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> | |
| 51 </repeat> | |
| 52 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" | |
| 53 label="Visualising the analysis results" | |
| 54 help="output an additional PDF files" /> | |
| 55 <param name="format" type="select" label="Output Format"> | |
| 56 <option value="bed">BED</option> | |
| 57 <option value="gff">GFF</option> | |
| 58 <option value="wig">WIG</option> | |
| 59 </param> | |
| 60 </inputs> | |
| 61 <configfiles> | |
| 62 <configfile name="infile"> | |
| 63 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks | |
| 64 #set $counter = 1 | |
| 65 #for $sample in $samples: | |
| 66 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks | |
| 67 #set $counter = $counter + 1 | |
| 68 #end for | |
| 69 </configfile> | |
| 70 </configfiles> | |
| 71 <outputs> | |
| 72 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> | |
| 73 <change_format> | |
| 74 <when input="format" value="wig" format="wig" /> | |
| 75 <when input="format" value="gff" format="gff" /> | |
| 76 </change_format> | |
| 77 </data> | |
| 78 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> | |
| 79 <filter>pdf == True</filter> | |
| 80 </data> | |
| 81 </outputs> | |
| 82 | |
| 83 <help> | |
| 84 | |
| 85 .. class:: infomark | |
| 86 | |
| 87 **What it does** | |
| 88 | |
| 89 | |
| 90 ------ | |
| 91 | |
| 92 **References** | |
| 93 | |
| 94 DiffBind_ Authors: Rory Stark, Gordon Brown | |
| 95 | |
| 96 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html | |
| 97 | |
| 98 Wrapper authors: Bjoern Gruening, Pavankumar Videm | |
| 99 | |
| 100 </help> | |
| 101 </tool> |