Mercurial > repos > miller-lab > genome_diversity
comparison rank_pathways.xml @ 10:9b92372de9f6
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 |
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| 9:22fe0154fa54 | 10:9b92372de9f6 |
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| 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 |