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comparison tools/oncodrivefm_tool/oncodrivefm_tool.xml @ 2:09f9829f1400

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author Saket Choudhary <saketkc@gmail.com>
date Wed, 20 Nov 2013 01:47:49 +0530
parents 386fa4776fde
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1:386fa4776fde 2:09f9829f1400
1 <tool id="oncodrivefm_tool" name="OncodriveFM"> 1 <tool id="oncodrivefm_tool" name="OncodriveFM">
2 <description>OncodriveFM </description> 2 <description>OncodriveFM </description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.1">requests</requirement> 4 <requirement type="package" version="2.0.1">requests</requirement>
5 </requirements> 5 </requirements>
6 <tool_dependency>
7 <package name="oncodrivefm">
8 <install version="0.6-dev">
9 <actions>
10 <action type="setup_virtualenv">distribute</action>
11 <action type="setup_virtualenv">python-dateutil==2.1</action>
12 <action type="setup_virtualenv">pytz==2013b</action>
13 <action type="setup_virtualenv">numpy==1.7.1</action>
14 <action type="setup_virtualenv">scipy==0.12.0</action>
15 <action type="setup_virtualenv">pandas==0.12.0</action>
16 <action type="setup_virtualenv">statsmodels==0.4.3</action>
17 <action type="setup_virtualenv">https://bitbucket.org/bbglab/oncodrivefm/get/master.tar.gz</action>
18 </actions>
19 </install>
20 <readme>OncodriveFm avalable at https://bitbucket.org/bbglab/oncodrivefm/</readme>
21 </package>
22 </tool_dependency>
23 6
24 <command interpreter="python"> 7 <command interpreter="python">
25 #if $mappingpathcondition.hasmapfile=="yes" 8 #if $mappingpathcondition.hasmapfile=="yes"
26 oncodrivefm_tool.py -N $samplings -e $estimator --gt $gene_threshold --pt $pathway_threshold -s $slices -m $mapping_path -o1 $output1 -o2 $output2 -i $input 9 oncodrivefm_tool.py -N $samplings -e $estimator --gt $gene_threshold --pt $pathway_threshold -s $slices -m $mapping_path -o1 $output1 -o2 $output2 -i $input
27 #else 10 #else