Mercurial > repos > bornea > prohits_dotplot_generator

Binary file prohits_dotplot_generator/Dotplot_Release.tar.gz has changed
--- a/prohits_dotplot_generator/GNU Free Documentation License.txt	Tue Mar 15 16:45:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,451 +0,0 @@
-
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--- a/prohits_dotplot_generator/ProHits_DotPlot_Generator.py	Tue Mar 15 16:45:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-#######################################################################################
-# Python-code: Dotplot Runner
-# Author: Adam L Borne
-# Contributers: Paul A Stewart, Brent Kuenzi
-#######################################################################################
-# This script runs the dotplot program found at http://prohitstools.mshri.on.ca/.
-#######################################################################################
-# Copyright (C)  Adam Borne.
-# Permission is granted to copy, distribute and/or modify this document
-# under the terms of the GNU Free Documentation License, Version 1.3
-# or any later version published by the Free Software Foundation;
-# with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
-# A copy of the license is included in the section entitled "GNU
-# Free Documentation License".
-#######################################################################################
-## REQUIRED INPUT ##
-
-# 1) list_file: SaintExpress output file.
-# 2) FDR1: Primary false discovery rate. (default = 0.01)
-# 3) FDR2: Secondary false discovery rate. (default = 0.025)
-# 4) spec_max: Maximum spectral count. (default = 50)
-#######################################################################################
-import os
-import os
-import sys
-
-
-FDR1 = sys.argv[2]
-FDR2 = sys.argv[3]
-spec_max = sys.argv[4]
-os.rename(sys.argv[1], "saint_input.txt")
-ins_path = sys.argv[9]
-
-dirs_list = []
-for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
-    dirs_list.extend(dirnames)
-    break
-if r"Dotplot_Release" in dirs_list:
-    pass
-else:
-    cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz"
-    os.system(cmd)
-
-
-cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) +
-    r" -t " + str(FDR2) + " -m " + str(spec_max))
-os.system(cmd)
-
-cmd1 = r"cp -a ./Output_saint_input/. ."
-os.system(cmd1)
-
-os.rename("saint_input.txt", str(sys.argv[1]))
-os.rename('dotplot.pdf', str(sys.argv[5]))
-os.rename('bait2bait.pdf', str(sys.argv[6]))
-os.rename('estimated.pdf', str(sys.argv[7]))
-os.rename('stats.pdf', str(sys.argv[8]))
\ No newline at end of file
--- a/prohits_dotplot_generator/ProHits_DotPlot_Generator.xml	Tue Mar 15 16:45:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +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</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"/>
-  </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
--- a/prohits_dotplot_generator/tool_dependencies.xml	Tue Mar 15 16:45:20 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="INSTALL_RUN_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-</tool_dependency>
\ No newline at end of file