Mercurial > repos > s-kaufmann > synteny_mapper

comparison visualization.xml @ 10:a6c5e5a41025 draft

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Uploaded
author s-kaufmann
date Fri, 15 Aug 2014 08:35:52 -0400
parents 8a4190457eb7
children 25ec18816c91
comparison
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9:dd2fdd397831 10:a6c5e5a41025
3 3
4 <requirements> 4 <requirements>
5 <requirement type="set_environment">JAR_PATH</requirement> 5 <requirement type="set_environment">JAR_PATH</requirement>
6 <requirement type="package" version="0.64">circos</requirement> 6 <requirement type="package" version="0.64">circos</requirement>
7 <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement> 7 <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
8 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
9 <requirement type="set_environment">R_PATH</requirement>
8 </requirements> 10 </requirements>
9 11
10 <command> 12 <command>
11 java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path 13 java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path $linear \$R_PATH
12 </command> 14 </command>
13 15
14 <inputs> 16 <inputs>
15 <param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/> 17 <param name="mappingFile" format="tabular" type="data" label="Mapped genes (SyntenyMapper output1)"/>
16 <param name="syntenyFile" format="tabular" type="data" size="9" label="Refined synteny regions (SyntenyMapper output2)"/> 18 <param name="syntenyFile" format="tabular" type="data" size="9" label="Refined synteny regions (SyntenyMapper output2)"/>
20 <column name="value" index="0"/> 22 <column name="value" index="0"/>
21 <!--<filter type="static_value" name="regular" value="regular" column="9"/> 23 <!--<filter type="static_value" name="regular" value="regular" column="9"/>
22 <validator type="expression">str(value).find("000") != -1</validator>--> 24 <validator type="expression">str(value).find("000") != -1</validator>-->
23 <filter type="sort_by" column="0" ref="syntenyFile"/> 25 <filter type="sort_by" column="0" ref="syntenyFile"/>
24 </options> 26 </options>
27 </param>
28 <param name="linear" type="select" label="Linear">
29 <option value="false">Circular representation</option>
30 <option value="true">Linear representation</option>
25 </param> 31 </param>
26 </inputs> 32 </inputs>
27 <outputs> 33 <outputs>
28 <data format="html" name="out_file1" label="Visualization of Mapping"/> 34 <data format="html" name="out_file1" label="Visualization of Mapping"/>
29 </outputs> 35 </outputs>