Mercurial > repos > miller-lab > genome_diversity
annotate pathway_image.xml @ 7:e29f4d801bb0
change wsf -> snp; wpf -> sap
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 18 Apr 2012 11:12:21 -0400 |
| parents | 2c498d40ecde |
| children | 9b92372de9f6 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_pathway_image" name="Generate" version="1.0.0"> |
| 2 <description>KEGG pathway images</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> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
14 <param name="input" type="data" format="sap" label="Table"> |
| 0 | 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> | |
|
7
e29f4d801bb0
change wsf -> snp; wpf -> sap
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
|
32 <param name="input" value="test_in/sample.sap" ftype="sap" /> |
| 0 | 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 **What it does** | |
| 40 | |
| 41 This tool produces an image of an input KEGG pathway, highlighting the | |
| 42 modules representing genes in an input list. NOTE: a given gene can | |
| 43 be assigned to multiple modules, and different genes can be assigned to | |
| 44 the same module. | |
| 45 </help> | |
| 46 </tool> |