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comparison multigps.xml @ 1:7779952f00dd draft

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Uploaded
author greg
date Wed, 23 Dec 2015 10:14:53 -0500
parents 269f8d00045c
children f52d31a2c386
comparison
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0:269f8d00045c 1:7779952f00dd
5 <requirement type="package" version="3.11.0">edger</requirement> 5 <requirement type="package" version="3.11.0">edger</requirement>
6 <requirement type="package" version="2.14">biocbasics</requirement> 6 <requirement type="package" version="2.14">biocbasics</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ## when I don't run on my mac...
11 ## java -Xmx20G -jar $__tool_directory__/multigps_v0.5.jar
12 mkdir multigps_out && 10 mkdir multigps_out &&
13 java -jar $__tool_directory__/multigps_v0.5.jar 11 java -jar $__tool_directory__/multigps_v0.5.jar
14 --threads="\${GALAXY_SLOTS:-4}" 12 --threads="\${GALAXY_SLOTS:-4}"
15 --verbose 13 --verbose
16 --geninfo ${chromInfo} 14 --geninfo ${chromInfo}
28 ]]> 26 ]]>
29 </command> 27 </command>
30 <configfiles> 28 <configfiles>
31 <configfile name="design_file"> 29 <configfile name="design_file">
32 <![CDATA[ 30 <![CDATA[
33 #for input in $input_files: 31 #for input in $input_files:
34 #set filename = "{$input['input'].filename}" 32 #set filename = "{$input['input'].filename}"
35 #set signal_control = $input['signal_control'] 33 #set signal_control = $input['signal_control']
36 #set format = $input['input'].ext 34 #set format = $input['input'].ext
37 #set condition_name = $input['condition_name'] 35 #set condition_name = $input['condition_name']
38 #set replicate_name = $input['replicate_name'] 36 #set replicate_name = $input['replicate_name']
39 #set line = '\t'.join($filename, $signal_control, $format, $condition_name, $replicate_name]) 37 #set line = '\t'.join($filename, $signal_control, $format, $condition_name, $replicate_name])
40 ${line} 38 ${line}
41 #end for 39 #end for
42 ]]> 40 ]]>
43 </configfile> 41 </configfile>
44 <configfile name="get_seq_dir"> 42 <configfile name="get_seq_dir">
45 <![CDATA[ 43 <![CDATA[
46 #!/usr/bin/env python 44 #!/usr/bin/env python