Mercurial > repos > bgruening > diffbind
comparison diffbind.xml @ 9:20c431b4cf74 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 14 Jan 2014 18:07:20 -0500 |
| parents | da65ae70e2e1 |
| children | b1b96b6ed60c |
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| 8:7929c8b3f6f9 | 9:20c431b4cf74 |
|---|---|
| 11 diffbind.R | 11 diffbind.R |
| 12 -i $infile | 12 -i $infile |
| 13 -o $outfile | 13 -o $outfile |
| 14 -p $plots | 14 -p $plots |
| 15 -f $format | 15 -f $format |
| 16 ; | |
| 17 cat $infile; | |
| 16 </command> | 18 </command> |
| 17 <stdio> | 19 <stdio> |
| 18 <regex match="Execution halted" | 20 <regex match="Execution halted" |
| 19 source="both" | 21 source="both" |
| 20 level="fatal" | 22 level="fatal" |
| 47 <option value="gff">GFF</option> | 49 <option value="gff">GFF</option> |
| 48 <option value="wig">WIG</option> | 50 <option value="wig">WIG</option> |
| 49 </param> | 51 </param> |
| 50 </inputs> | 52 </inputs> |
| 51 <configfiles> | 53 <configfiles> |
| 52 <configfile name="infile"> | 54 <configfile name="infile"> |
| 53 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks | 55 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks |
| 54 #for $sample in $samples: | 56 #for $sample in $samples: |
| 55 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks | 57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks |
| 56 #end for | 58 #end for |
| 57 </configfile> | 59 </configfile> |
| 58 </configfiles> | 60 </configfiles> |
| 59 <outputs> | 61 <outputs> |
| 60 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> | 62 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> |
| 61 <change_format> | 63 <change_format> |
| 62 <when input="format" value="wig" format="wig" /> | 64 <when input="format" value="wig" format="wig" /> |
| 63 <when input="format" value="gff" format="gff" /> | 65 <when input="format" value="gff" format="gff" /> |
| 64 </change_format> | 66 </change_format> |
| 65 </data> | 67 </data> |
| 66 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> | 68 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> |
| 67 <filter>pdf == True</filter> | 69 <filter>pdf == True</filter> |
| 68 </data> | 70 </data> |
| 69 </outputs> | 71 </outputs> |
| 70 | 72 |
| 71 <help> | 73 <help> |