Mercurial > repos > bornea > prohits_dotplot_generator
view ProHits_DotPlot_Generator.xml @ 28:213e87eb9ade draft
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author | bornea |
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date | Tue, 19 Apr 2016 11:57:16 -0400 |
parents | c0b883652821 |
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<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="DotPlot did not run correctly" source="stdout" level="fatal" description="DotPlot did not run correctly."/> <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"/> </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> Prohits Dotplot --------------- This tool 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/. Depending on your Galaxy distribution, this tool may take a few minutes to run. **1) SAINT Output File** SAINTexpress generated *list.txt* file **2) False Discovery Rate 1** Primary FDR cutoff in range 0-1 (default 0.01) **3) False Discovery Rate 2** Secondary FDR cutoff; must be higher than the primary (default 0.025) **4) Maximum Spectral Count** Maximum spectral count to visualize (default 50) ---------------- **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>