Mercurial > repos > bornea > prohits_dotplot_generator

comparison ProHits_DotPlot_Generator.xml @ 23:fbc857f87f52 draft

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author bornea
date Mon, 18 Apr 2016 10:49:29 -0400
parents 609ecf4d57fe
children f0410eccdc33
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22:609ecf4d57fe 23:fbc857f87f52
40 <param name="input" value="fa_gc_content_input.fa"/> 40 <param name="input" value="fa_gc_content_input.fa"/>
41 <output name="out_file1" file="fa_gc_content_output.txt"/> 41 <output name="out_file1" file="fa_gc_content_output.txt"/>
42 </test> 42 </test>
43 </tests> 43 </tests>
44 <help> 44 <help>
45 **Running ProHits DotPlot** 45 Prohits Dotplot
46 --------------
46 47
47 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. 48 This tool runs the biclustering version of the DotPlot tool found
49 at http://prohitstools.mshri.on.ca/. A more interactive version
50 can be found at http://prohits-viz.lunenfeld.ca/. Depending on
51 your Galaxy distribution, this tool may take a few minutes to run.
48 52
49 INPUTS: 53 **1) SAINT Output File**
50 54
51 Saint Output: SAINTexpress generated "list.txt" file. 55 SAINTexpress generated *list.txt* file
52 56
53 Primary False Discovery Rate 57 **2) False Discovery Rate 1**
54 58
55 Secondary False Discovery Rate 59 Primary FDR cutoff in range 0-1 (default 0.01)
56 60
57 Maximum Spectral Count 61 **3) False Discovery Rate 2**
58 62
59 ------ 63 Secondary FDR cutoff; must be higher than the primary (default 0.025)
64
65 **4) Maximum Spectral Count**
66
67 Maximum spectral count to visualize (default 50)
60 68
61 **Please cite** 69 **Please cite**
62 70
63 * 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. 71 * 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.
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