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comparison pathway_image.xml @ 21:d6b961721037

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Miller Lab Devshed version 4c04e35b18f6
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 05 Nov 2012 12:44:17 -0500
parents 8ae67e9fb6ff
children 66a183c44dd5
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20:8a4b8efbc82c 21:d6b961721037
4 <command interpreter="python"> 4 <command interpreter="python">
5 mkpthwpng.py 5 mkpthwpng.py
6 "--input=${input}" 6 "--input=${input}"
7 "--output=${output}" 7 "--output=${output}"
8 "--KEGGpath=${pathway}" 8 "--KEGGpath=${pathway}"
9 "--posKEGGclmn=${input.metadata.kegg_path}" 9 "--posKEGGclmn=${kpath}"
10 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}" 10 "--KEGGgeneposcolmn=${kgene}"
11 </command> 11 </command>
12 12
13 <inputs> 13 <inputs>
14 <param name="input" type="data" format="gd_sap" label="Table"> 14 <param name="input" type="data" format="tabular" label="Dataset" />
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" /> 15 <param name="kgene" type="data_column" data_ref="input" label="Column with KEGG gene ID" />
16 </param> 16 <param name="kpath" type="data_column" data_ref="input" numerical="false" label="Column with KEGG pathways" />
17 <param name="pathway" type="select"> 17 <param name="pathway" label="Pathway" type="select">
18 <options from_file="gd.pathways.txt"> 18 <options from_file="gd.pathways.txt">
19 <column name="value" index="1"/> 19 <column name="value" index="1"/>
20 <column name="name" index="2"/> 20 <column name="name" index="2"/>
21 <filter type="data_meta" ref="input" key="dbkey" column="0" separator="\t" /> 21 <filter type="data_meta" ref="input" key="dbkey" column="0" separator="\t" />
22 </options> 22 </options>
28 </outputs> 28 </outputs>
29 29
30 <tests> 30 <tests>
31 <test> 31 <test>
32 <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" /> 32 <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" />
33 <param name="kpath" value="10" />
34 <param name="kgene" value="12" />
33 <param name="pathway" value="cfa05214" /> 35 <param name="pathway" value="cfa05214" />
34 <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" /> 36 <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" />
35 </test> 37 </test>
36 </tests> 38 </tests>
37 39
38 <help> 40 <help>
39 41
42 **Dataset formats**
43
44 The input and output datasets are in tabular_ format.
45 The input dataset must have columns with KEGG gene ID and pathways.
46 The output dataset is described below.
47 (`Dataset missing?`_)
48
49 .. _tabular: ./static/formatHelp.html#tab
50 .. _Dataset missing?: ./static/formatHelp.html
51
52 -----
53
40 **What it does** 54 **What it does**
41 55
42 This tool produces an image of an input KEGG pathway, highlighting the 56 This tool produces an image of a KEGG pathway, highlighting (in red) the
43 modules representing genes in an input list. NOTE: a given gene can 57 modules representing genes in the input dataset. Click here_ for help
58 with reading the pathway map.
59
60 NOTE: a given gene can
44 be assigned to multiple modules, and different genes can be assigned to 61 be assigned to multiple modules, and different genes can be assigned to
45 the same module. 62 the same module.
46 63
64 .. _here: http://www.genome.jp/kegg/document/help_pathway.html
65
66 -----
67
68 **Example**
69
70 - input::
71
72 476153 probably damaging cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
73 483960 probably damaging N
74 610160 possibly damaging N
75 403657 benign cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04060=Cytokine-cytokine receptor interaction.cfa04144=Endocytosis.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04810=Regulation of actin cytoskeleton.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05212=Pancreatic cancer.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05218=Melanoma.cfa05219=Bladder cancer.cfa05223=Non-small cell lung cancer
76 etc.
77
78 output showing pathway cfa05214:
79
80 .. image:: ${static_path}/images/gd_pathway_image.png
81
47 </help> 82 </help>
48 </tool> 83 </tool>