Mercurial > repos > bgruening > diffbind

comparison diffbind.xml @ 9:20c431b4cf74 draft

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Uploaded
author bgruening
date Tue, 14 Jan 2014 18:07:20 -0500
parents da65ae70e2e1
children b1b96b6ed60c
comparison
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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>