Mercurial > repos > bgruening > diffbind

comparison diffbind.xml @ 11:a8dc71379df0 draft

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Uploaded
author bgruening
date Fri, 17 Jan 2014 04:04:16 -0500
parents b1b96b6ed60c
children 43884541e66f
comparison
equal deleted inserted replaced
10:b1b96b6ed60c 11:a8dc71379df0
4 <requirement type="binary">Rscript</requirement> 4 <requirement type="binary">Rscript</requirement>
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 <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</requirement>
9 </requirements> 10 </requirements>
10 <command> 11 <command>
11 ## seems that diffbind also needs file extensions to work properly 12 ## seems that diffbind also needs file extensions to work properly
12 #set $counter = 1 13 #set $counter = 1
13 #for $sample in $samples: 14 #for $sample in $samples:
16 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp; 17 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 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp;
18 #set $counter = $counter + 1 19 #set $counter = $counter + 1
19 #end for 20 #end for
20 21
21 Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R 22 Rscript \$AUGUSTUS_SCRIPT_PATH/diffbind.R
22 -i $infile 23 -i $infile
23 -o $outfile 24 -o $outfile
24 -p $plots 25 -p $plots
25 -f $format 26 -f $format
26 </command> 27 </command>