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comparison ProHits_DotPlot_Generator.xml @ 15:a6c081fcc0a9 draft

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author bornea
date Wed, 16 Mar 2016 12:10:35 -0400
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1 <tool id="ProHits_DotPlot_Generator" name="ProHits DotPlot Generator">
2 <description></description>
3 <command interpreter="python">ProHits_DotPlot_Generator.py $saint_file $FDR1 $FDR2 $spec_max $dotplot $heatmap $estimated $stats</command>
4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements>
7 <inputs>
8 <param format="txt" name="saint_file" type="data" label="SAINT Output"/>
9 <param type="float" name="FDR1" label="False Discovery Rate 1" value="0.01"/>
10 <param type="float" name="FDR2" label="False Discovery Rate 2" value="0.025"/>
11 <param type="integer" name="spec_max" label="Maximum spectral count" value="50"/>
12 </inputs>
13 <outputs>
14 <data format="pdf" name="dotplot" label="DotPlot" />
15 <data format="pdf" name="heatmap" label="Heatmap" />
16 <data format="pdf" name="estimated" label="Estimated" />
17 <data format="pdf" name="stats" label="Stats" />
18 </outputs>
19 <stdio>
20 <regex match="Error|error"
21 source="stdout"
22 level="fatal"
23 description="Unknown error"/>
24 <regex match="Error|error"
25 source="stderr"
26 level="fatal"
27 description="Unknown error"/>
28 <regex match="Error: bad bait"
29 source="stdout"
30 level="fatal"
31 description="Error: bad bait"/>
32 </stdio>
33
34 <tests>
35 <test>
36 <param name="input" value="fa_gc_content_input.fa"/>
37 <output name="out_file1" file="fa_gc_content_output.txt"/>
38 </test>
39 </tests>
40 <help>
41 **Running ProHits DotPlot**
42
43 This runs the biclustering version of the DotPlot tool found at http://prohitstools.mshri.on.ca/. A more interactive version can be found at http://prohits-viz.lunenfeld.ca/. This script will take a long time to run.
44
45 INPUTS:
46
47 Saint Output: SAINTexpress generated "list.txt" file.
48
49 Primary False Discovery Rate
50
51 Secondary False Discovery Rate
52
53 Maximum Spectral Count
54
55 ------
56
57 **Please cite**
58
59 * Knight, J.D., Liu, G., Zhang, J., Pasculescu, A., Choi, H., and Gingras, A.-C. (2014) A web-tool for visualizing quantitative protein-protein interaction data. Proteomics, in press. PMID:25422071.
60
61 </help>
62 </tool>