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comparison pathway_image.xml @ 12:4b6590dd7250

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author miller-lab
date Wed, 12 Sep 2012 17:10:26 -0400
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11:d4ec09e8079f 12:4b6590dd7250
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>
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 **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>