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comparison diffbind.xml @ 10:b1b96b6ed60c draft

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author bgruening
date Thu, 16 Jan 2014 04:17:16 -0500
parents 20c431b4cf74
children a8dc71379df0
comparison
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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"# &amp;&amp;
15 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp;
16 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp;
17 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp;
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}">