Mercurial > repos > miller-lab > genome_diversity
comparison pathway_image.xml @ 17:a3af29edcce2
Uploaded Miller Lab Devshed version a51c894f5bed
| author | miller-lab |
|---|---|
| date | Fri, 28 Sep 2012 11:57:18 -0400 |
| parents | 8ae67e9fb6ff |
| children | d6b961721037 |
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| 16:be0e2223c531 | 17:a3af29edcce2 |
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| 1 <tool id="gd_pathway_image" name="Pathway Image" version="1.0.0"> | |
| 2 <description>: Draw a KEGG pathway, highlighting specified gene modules</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 mkpthwpng.py | |
| 6 "--input=${input}" | |
| 7 "--output=${output}" | |
| 8 "--KEGGpath=${pathway}" | |
| 9 "--posKEGGclmn=${input.metadata.kegg_path}" | |
| 10 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}" | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param name="input" type="data" format="gd_sap" label="Table"> | |
| 15 <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" /> | |
| 16 </param> | |
| 17 <param name="pathway" type="select"> | |
| 18 <options from_file="gd.pathways.txt"> | |
| 19 <column name="value" index="1"/> | |
| 20 <column name="name" index="2"/> | |
| 21 <filter type="data_meta" ref="input" key="dbkey" column="0" separator="\t" /> | |
| 22 </options> | |
| 23 </param> | |
| 24 </inputs> | |
| 25 | |
| 26 <outputs> | |
| 27 <data name="output" format="png" /> | |
| 28 </outputs> | |
| 29 | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" /> | |
| 33 <param name="pathway" value="cfa05214" /> | |
| 34 <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 | |
| 38 <help> | |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 This tool produces an image of an input KEGG pathway, highlighting the | |
| 43 modules representing genes in an input list. NOTE: a given gene can | |
| 44 be assigned to multiple modules, and different genes can be assigned to | |
| 45 the same module. | |
| 46 | |
| 47 </help> | |
| 48 </tool> |