# HG changeset patch
# User bornea
# Date 1460669025 14400
# Node ID 9329d9ec60b042cb5f7308f8b4498f5a37838574
# Parent  2c991a36347aed39cec827c27ac48ccc9c07ab69
Deleted selected files

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
@@ -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