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ProHits_DotPlot_Generator.xml |
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| diff -r 72fe77df329b -r 2c991a36347a ProHits_DotPlot_Generator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ProHits_DotPlot_Generator.xml Thu Apr 14 16:51:07 2016 -0400 |
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| @@ -0,0 +1,66 @@ +<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 |