Mercurial > repos > bgruening > diffbind
comparison diffbind.xml @ 10:b1b96b6ed60c draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 16 Jan 2014 04:17:16 -0500 |
| parents | 20c431b4cf74 |
| children | a8dc71379df0 |
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| 9:20c431b4cf74 | 10:b1b96b6ed60c |
|---|---|
| 5 <requirement type="R-module">DESeq2</requirement> | 5 <requirement type="R-module">DESeq2</requirement> |
| 6 <requirement type="package" version="3.0.1">R_3_0_1</requirement> | 6 <requirement type="package" version="3.0.1">R_3_0_1</requirement> |
| 7 <requirement type="package" version="1.0.17">deseq2</requirement> | 7 <requirement type="package" version="1.0.17">deseq2</requirement> |
| 8 <requirement type="package" version="1.8.3">diffbind</requirement> | 8 <requirement type="package" version="1.8.3">diffbind</requirement> |
| 9 </requirements> | 9 </requirements> |
| 10 <command interpreter="Rscript"> | 10 <command> |
| 11 diffbind.R | 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 | |
| 12 -i $infile | 22 -i $infile |
| 13 -o $outfile | 23 -o $outfile |
| 14 -p $plots | 24 -p $plots |
| 15 -f $format | 25 -f $format |
| 16 ; | |
| 17 cat $infile; | |
| 18 </command> | 26 </command> |
| 19 <stdio> | 27 <stdio> |
| 20 <regex match="Execution halted" | 28 <regex match="Execution halted" |
| 21 source="both" | 29 source="both" |
| 22 level="fatal" | 30 level="fatal" |
| 51 </param> | 59 </param> |
| 52 </inputs> | 60 </inputs> |
| 53 <configfiles> | 61 <configfiles> |
| 54 <configfile name="infile"> | 62 <configfile name="infile"> |
| 55 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks | 63 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks |
| 64 #set $counter = 1 | |
| 56 #for $sample in $samples: | 65 #for $sample in $samples: |
| 57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks | 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 | |
| 58 #end for | 68 #end for |
| 59 </configfile> | 69 </configfile> |
| 60 </configfiles> | 70 </configfiles> |
| 61 <outputs> | 71 <outputs> |
| 62 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> | 72 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> |