| Previous changeset 18:2c991a36347a (2016-04-14) Next changeset 20:0ac97a6298c2 (2016-04-14) |
|
Commit message:
Deleted selected files |
|
removed:
ProHits_DotPlot_Generator.xml |
| b |
| diff -r 2c991a36347a -r 9329d9ec60b0 ProHits_DotPlot_Generator.xml --- a/ProHits_DotPlot_Generator.xml Thu Apr 14 16:51:07 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,66 +0,0 @@ -<tool id="ProHits_DotPlot_Generator" name="ProHits DotPlot Generator"> - <description></description> - <command interpreter="python">ProHits_DotPlot_Generator.py $saint_file $FDR1 $FDR2 $spec_max $dotplot $heatmap $estimated $stats \$INSTALL_RUN_PATH/</command> - <requirements> - <requirement type="set_environment">INSTALL_RUN_PATH</requirement> - </requirements> - <inputs> - <param format="txt" name="saint_file" type="data" label="SAINT Output"/> - <param type="float" name="FDR1" label="False Discovery Rate 1" value="0.01"/> - <param type="float" name="FDR2" label="False Discovery Rate 2" value="0.025"/> - <param type="integer" name="spec_max" label="Maximum spectral count" value="50"/> - </inputs> - <outputs> - <data format="pdf" name="dotplot" label="DotPlot" /> - <data format="pdf" name="heatmap" label="Heatmap" /> - <data format="pdf" name="estimated" label="Estimated" /> - <data format="pdf" name="stats" label="Stats" /> - </outputs> - <stdio> - <regex match="Error|error" - source="stdout" - level="fatal" - description="Unknown error"/> - <regex match="Error|error" - source="stderr" - level="fatal" - description="Unknown error"/> - <regex match="Error: bad bait" - source="stdout" - level="fatal" - description="Error: bad bait"/> - <regex match="os.rename(sys." - source="stdout" - level="fatal" - description="Database association broken please reupload file"/> - </stdio> - - <tests> - <test> - <param name="input" value="fa_gc_content_input.fa"/> - <output name="out_file1" file="fa_gc_content_output.txt"/> - </test> - </tests> - <help> -**Running ProHits DotPlot** - -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. - -INPUTS: - -Saint Output: SAINTexpress generated "list.txt" file. - -Primary False Discovery Rate - -Secondary False Discovery Rate - -Maximum Spectral Count - ------- - -**Please cite** - - * 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. - - </help> -</tool> \ No newline at end of file |