Mercurial > repos > miller-lab > genome_diversity

comparison rank_pathways.xml @ 10:9b92372de9f6

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rename snp to gsSnp, sap to gdSap
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 04 Sep 2012 12:49:53 -0400
parents e29f4d801bb0
children
comparison
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9:22fe0154fa54 10:9b92372de9f6
14 "--posKEGGclmn=${input.metadata.kegg_path}" 14 "--posKEGGclmn=${input.metadata.kegg_path}"
15 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}" 15 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}"
16 </command> 16 </command>
17 17
18 <inputs> 18 <inputs>
19 <param name="input" type="data" format="sap" label="Table"> 19 <param name="input" type="data" format="gdSap" label="Table">
20 <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" /> 20 <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" />
21 </param> 21 </param>
22 <param name="output_format" type="select" label="Output format"> 22 <param name="output_format" type="select" label="Output format">
23 <option value="a" selected="true">ranked by percentage of genes affected</option> 23 <option value="a" selected="true">ranked by percentage of genes affected</option>
24 <option value="b">ranked by change in length and number of paths</option> 24 <option value="b">ranked by change in length and number of paths</option>
29 <data name="output" format="tabular" /> 29 <data name="output" format="tabular" />
30 </outputs> 30 </outputs>
31 31
32 <tests> 32 <tests>
33 <test> 33 <test>
34 <param name="input" value="test_in/sample.sap" ftype="sap" /> 34 <param name="input" value="test_in/sample.gdSap" ftype="gdSap" />
35 <param name="output_format" value="a" /> 35 <param name="output_format" value="a" />
36 <output name="output" file="test_out/rank_pathways/rank_pathways.tabular" /> 36 <output name="output" file="test_out/rank_pathways/rank_pathways.tabular" />
37 </test> 37 </test>
38 </tests> 38 </tests>
39 39