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comparison ProteinInteractions.xml @ 6:830112c59150 draft

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author bornea
date Tue, 15 Mar 2016 15:36:37 -0400
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1 <tool id="SAINT_ProteinInteractions" name="SAINT Output to Protein Interaction File">
2 <description></description>
3 <command interpreter="python">ProteinInteractions.py $input $saint_cutoff $CPDB_cutoff $species $Cytoscape_File \$INSTALL_RUN_PATH/</command>
4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements>
7 <inputs>
8 <param format="txt" name="input" type="data" label="SAINT Output"/>
9 <param type="float" name="saint_cutoff" label="Saint Score Cutoff" value="0.8"/>
10 <param type="float" name="CPDB_cutoff" label="Consensus Path Database Score Cutoff" value="0.8"/>
11 <param type="select" name="species" label="Species">
12 <option value="Human">Human</option>
13 <option value="Yeast">Yeast</option>
14 <option value="Mouse">Mouse</option>
15 </param>
16 </inputs>
17 <outputs>
18 <data format="sif" name="Cytoscape_File" label="Cytoscape File"/>
19 </outputs>
20 <stdio>
21 <regex match="Error|error"
22 source="stdout"
23 level="fatal"
24 description="Unknown error"/>
25 <regex match="Error|error"
26 source="stderr"
27 level="fatal"
28 description="Unknown error"/>
29 <regex match="Error: bad bait"
30 source="stdout"
31 level="fatal"
32 description="Error: bad bait"/>
33 </stdio>
34
35 <tests>
36 <test>
37 <param name="input" value="fa_gc_content_input.fa"/>
38 <output name="out_file1" file="fa_gc_content_output.txt"/>
39 </test>
40 </tests>
41 <help>
42 **Protein Interactions**
43
44 This program will read in a SAINT 'list.txt' file and the interactions from ConsensusPathDB ( http://consensuspathdb.org/ ) and return all the interactions that we saw in our experiment in a format suitable for cytoscape. This allows us to filter before getting protein-protein interactions (PPI's) so that it doesn't affect our SAINT score or include interactions that don't score well.
45
46 INPUT
47
48 SAINT Output: SAINTexpress output.
49
50 SAINT Score Cutoff: Saint score cutoff for import (between 0 and 1).
51
52 Consensus Path Database Score Cutoff: Confidence of PPI from CPDB to include (between 0 and 1).
53 * low: no filtering
54 * medium: >0.5
55 * high: >0.7
56 * very high: >0.9
57
58 Species: Human, Yeast, or Mouse.
59
60 </help>
61 </tool>