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comparison diffbind.xml @ 1:0753d019a353 draft

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author bgruening
date Mon, 13 Jan 2014 17:58:55 -0500
parents 8d48d5591389
children 0c7207440cf0
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0:8d48d5591389 1:0753d019a353
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="2.13">diffbind</requirement> 8 <requirement type="package" version="2.13">diffbind</requirement>
9 </requirements> 9 </requirements>
10 <command interpreter="Rscript"> 10 <command interpreter="Rscript">
11 #import simplejson
12 diffbind.R 11 diffbind.R
13 -i $infile 12 -i $infile
14 -o $outfile 13 -o $outfile
15 -p $plots 14 -p $plots
16 -f $format 15 -f $format
56 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks 55 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks
57 #end for 56 #end for
58 </configfile> 57 </configfile>
59 </configfiles> 58 </configfiles>
60 <outputs> 59 <outputs>
61 <outputs>
62 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> 60 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
63 <change_format> 61 <change_format>
64 <when input="format" value="wig" format="wig" /> 62 <when input="format" value="wig" format="wig" />
65 <when input="format" value="gff" format="gff" /> 63 <when input="format" value="gff" format="gff" />
66 </change_format> 64 </change_format>