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prohits_dotplot_generator/Dotplot_Release.tar.gz prohits_dotplot_generator/GNU Free Documentation License.txt prohits_dotplot_generator/ProHits_DotPlot_Generator.py prohits_dotplot_generator/ProHits_DotPlot_Generator.xml prohits_dotplot_generator/tool_dependencies.xml |
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| diff -r 19fb3846b0cf -r 89783b79ef25 prohits_dotplot_generator/Dotplot_Release.tar.gz |
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| diff -r 19fb3846b0cf -r 89783b79ef25 prohits_dotplot_generator/GNU Free Documentation License.txt --- 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 |
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| b'@@ -1,451 +0,0 @@\n-\r\n- GNU Free Documentation License\r\n- Version 1.3, 3 November 2008\r\n-\r\n-\r\n- Copyright (C) 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc.\r\n- <http://fsf.org/>\r\n- Everyone is permitted to copy and distribute verbatim copies\r\n- of this license document, but changing it is not allowed.\r\n-\r\n-0. PREAMBLE\r\n-\r\n-The purpose of this License is to make a manual, textbook, or other\r\n-functional and useful document "free" in the sense of freedom: to\r\n-assure everyone the effective freedom to copy and redistribute it,\r\n-with or without modifying it, either commercially or noncommercially.\r\n-Secondarily, this License preserves for the author and publisher a way\r\n-to get credit for their work, while not being considered responsible\r\n-for modifications made by others.\r\n-\r\n-This License is a kind of "copyleft", which means that derivative\r\n-works of the document must themselves be free in the same sense. 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| diff -r 19fb3846b0cf -r 89783b79ef25 prohits_dotplot_generator/ProHits_DotPlot_Generator.py --- 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 |
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| @@ -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 |
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| diff -r 19fb3846b0cf -r 89783b79ef25 prohits_dotplot_generator/ProHits_DotPlot_Generator.xml --- 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 |
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| @@ -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 |
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| diff -r 19fb3846b0cf -r 89783b79ef25 prohits_dotplot_generator/tool_dependencies.xml --- 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 |
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| @@ -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 |