| Previous changeset 8:969fe96dbc7d (2016-03-15) Next changeset 10:19fb3846b0cf (2016-03-15) |
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Commit message:
Uploaded |
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added:
test_files/SC_SAINT_list.txt |
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removed:
test_files.7z toolshed_version/Dotplot_Release.tar.gz toolshed_version/GNU Free Documentation License.txt toolshed_version/ProHits_DotPlot_Generator.py toolshed_version/ProHits_DotPlot_Generator.xml toolshed_version/test_files.tar toolshed_version/test_files/SC_SAINT_list.txt toolshed_version/tool_dependencies.xml |
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| diff -r 969fe96dbc7d -r 7928f149bb99 test_files.7z |
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| Binary file test_files.7z has changed |
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| diff -r 969fe96dbc7d -r 7928f149bb99 test_files/SC_SAINT_list.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test_files/SC_SAINT_list.txt Tue Mar 15 16:39:57 2016 -0400 |
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| b'@@ -0,0 +1,473 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| diff -r 969fe96dbc7d -r 7928f149bb99 toolshed_version/GNU Free Documentation License.txt --- a/toolshed_version/GNU Free Documentation License.txt Tue Mar 15 16:39:22 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. It\r\n-complements the GNU General Public License, which is a copyleft\r\n-license designed for free software.\r\n-\r\n-We have designed this License in order to use it for manuals for free\r\n-software, because free software needs free documentation: a free\r\n-program should come with manuals providing the same freedoms that the\r\n-software does. But this License is not limited to software manuals;\r\n-it can be used for any textual work, regardless of subject matter or\r\n-whether it is published as a printed book. We recommend this License\r\n-principally for works whose purpose is instruction or reference.\r\n-\r\n-\r\n-1. APPLICABILITY AND DEFINITIONS\r\n-\r\n-This License applies to any manual or other work, in any medium, that\r\n-contains a notice placed by the copyright holder saying it can be\r\n-distributed under the terms of this License. Such a notice grants a\r\n-world-wide, royalty-free license, unlimited in duration, to use that\r\n-work under the conditions stated herein. The "Document", below,\r\n-refers to any such manual or work. Any member of the public is a\r\n-licensee, and is addressed as "you". You accept the license if you\r\n-copy, modify or distribute the work in a way requiring permission\r\n-under copyright law.\r\n-\r\n-A "Modified Version" of the Document means any work containing the\r\n-Document or a portion of it, either copied verbatim, or with\r\n-modifications and/or translated into another language.\r\n-\r\n-A "Secondary Section" is a named appendix or a front-matter section of\r\n-the Document that deals exclusively with the relationship of the\r\n-publishers or authors of the Document to the Document\'s overall\r\n-subject (or to related matters) and contains nothing that could fall\r\n-directly within that overall subject. 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See\r\n-http://www.gnu.org/copyleft/.\r\n-\r\n-Each version of the License is given a distinguishing version number.\r\n-If the Document specifies that a particular numbered version of this\r\n-License "or any later version" applies to it, you have the option of\r\n-following the terms and conditions either of that specified version or\r\n-of any later version that has been published (not as a draft) by the\r\n-Free Software Foundation. If the Document does not specify a version\r\n-number of this License, you may choose any version ever published (not\r\n-as a draft) by the Free Software Foundation. If the Document\r\n-specifies that a proxy can decide which future versions of this\r\n-License can be used, that proxy\'s public statement of acceptance of a\r\n-version permanently authorizes you to choose that version for the\r\n-Document.\r\n-\r\n-11. 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| diff -r 969fe96dbc7d -r 7928f149bb99 toolshed_version/ProHits_DotPlot_Generator.py --- a/toolshed_version/ProHits_DotPlot_Generator.py Tue Mar 15 16:39:22 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 969fe96dbc7d -r 7928f149bb99 toolshed_version/ProHits_DotPlot_Generator.xml --- a/toolshed_version/ProHits_DotPlot_Generator.xml Tue Mar 15 16:39:22 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,31 +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> - <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" - source="stdout" - level="fatal" - description="Unknown error"/> - </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> - </help> -</tool> \ No newline at end of file |
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| diff -r 969fe96dbc7d -r 7928f149bb99 toolshed_version/test_files/SC_SAINT_list.txt --- a/toolshed_version/test_files/SC_SAINT_list.txt Tue Mar 15 16:39:22 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,473 +0,0 @@\n-Bait\tPrey\tPreyGene\tSpec\tSpecSum\tAvgSpec\tNumReplicates\tctrlCounts\tAvgP\tMaxP\tTopoAvgP\tTopoMaxP\tSaintScore\tlogOddsScore\tFoldChange\tBFDR\tboosted_by\n-WT_EGFR\tEGFR_HUMAN\tEGFR\t67|52|45|55\t219\t54.75\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t68.87\t547.50\t0.00\t\n-WT_EGFR\tERBB2_HUMAN\tERBB2\t4|5|3|5\t17\t4.25\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t42.50\t0.00\t\n-WT_EGFR\tP85B_HUMAN\tPIK3R2\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tP55G_HUMAN\tPIK3R3\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tP85A_HUMAN\tPIK3R1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tK2C1_HUMAN\tKRT1\t3|4|6|5\t18\t4.50\t4\t10|10|7|7\t0.00\t0.00\t0.00\t0.00\t0.00\t-27.06\t0.53\t0.51\t\n-WT_EGFR\tK1C10_HUMAN\tKRT10\t2|0|3|3\t8\t2.00\t4\t1|2|4|3\t0.01\t0.02\t0.01\t0.02\t0.01\t-9.56\t0.80\t0.49\t\n-WT_EGFR\tK1C16_HUMAN\tKRT16\t0|0|2|1\t3\t0.75\t4\t1|1|2|2\t0.03\t0.12\t0.03\t0.12\t0.03\t-5.35\t0.50\t0.47\t\n-WT_EGFR\tGRB2_HUMAN\tGRB2\t2|0|2|2\t6\t1.50\t4\t0|0|0|0\t0.74\t0.99\t0.74\t0.99\t0.74\t-0.11\t15.00\t0.05\t\n-WT_EGFR\tGRP78_HUMAN\tHSPA5\t16|14|11|12\t53\t13.25\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t19.16\t132.50\t0.00\t\n-WT_EGFR\tK22E_HUMAN\tKRT2\t2|3|6|4\t15\t3.75\t4\t4|4|1|1\t0.15\t0.50\t0.15\t0.50\t0.15\t-5.61\t1.50\t0.44\t\n-WT_EGFR\tK2C8_HUMAN\tKRT8\t1|1|2|2\t6\t1.50\t4\t0|0|0|0\t0.49\t0.99\t0.49\t0.99\t0.49\t2.40\t15.00\t0.19\t\n-WT_EGFR\tK2C5_HUMAN\tKRT5\t1|1|3|2\t7\t1.75\t4\t1|1|2|0\t0.29\t0.74\t0.29\t0.74\t0.29\t-1.74\t1.75\t0.26\t\n-WT_EGFR\tK2C4_HUMAN\tKRT4\t0|0|0|0\t0\t0.00\t4\t0|1|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.65\t0.00\t0.51\t\n-WT_EGFR\tK2C6B_HUMAN\tKRT6B\t1|2|4|4\t11\t2.75\t4\t2|2|2|1\t0.25\t0.47\t0.25\t0.47\t0.25\t-4.44\t1.57\t0.42\t\n-WT_EGFR\tK2C7_HUMAN\tKRT7\t0|0|0|2\t2\t0.50\t4\t0|0|0|0\t0.25\t0.99\t0.25\t0.99\t0.25\t-0.11\t5.00\t0.28\t\n-WT_EGFR\tHSP7C_HUMAN\tHSPA8\t15|10|12|11\t48\t12.00\t4\t0|0|1|1\t1.00\t1.00\t1.00\t1.00\t1.00\t12.83\t24.00\t0.00\t\n-WT_EGFR\tPK3CA_HUMAN\tPIK3CA\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tERBB3_HUMAN\tERBB3\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tADT2_HUMAN\tSLC25A5\t5|3|5|5\t18\t4.50\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t45.00\t0.00\t\n-WT_EGFR\tADT3_HUMAN\tSLC25A6\t5|4|5|5\t19\t4.75\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t8.02\t47.50\t0.00\t\n-WT_EGFR\tK1C9_HUMAN\tKRT9\t1|1|1|0\t3\t0.75\t4\t0|0|1|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.65\t3.00\t0.51\t\n-WT_EGFR\tTBA1A_HUMAN\tTUBA1A\t5|3|5|3\t16\t4.00\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t40.00\t0.00\t\n-WT_EGFR\tTBA4A_HUMAN\tTUBA4A\t3|2|3|1\t9\t2.25\t4\t0|0|0|0\t0.75\t1.00\t0.75\t1.00\t0.75\t2.40\t22.50\t0.02\t\n-WT_EGFR\tARHG5_HUMAN\tARHGEF5\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tPK3CB_HUMAN\tPIK3CB\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tIRS1_HUMAN\tIRS1\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tTBB5_HUMAN\tTUBB\t8|6|5|2\t21\t5.25\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t4.43\t52.50\t0.00\t\n-WT_EGFR\tTBB3_HUMAN\tTUBB3\t2|2|3|1\t8\t2.00\t4\t0|0|0|0\t0.74\t1.00\t0.74\t1.00\t0.74\t2.40\t20.00\t0.05\t\n-WT_EGFR\tHS90A_HUMAN\tHSP90AA1\t3|3|1|2\t9\t2.25\t4\t0|0|0|0\t0.75\t1.00\t0.75\t1.00\t0.75\t2.40\t22.50\t0.02\t\n-WT_EGFR\tHS90B_HUMAN\tHSP90AB1\t4|2|1|2\t9\t2.25\t4\t0|0|0|0\t0.74\t1.00\t0.74\t1.00\t0.74\t2.40\t22.50\t0.04\t\n-WT_EGFR\t1433E_HUMAN\tYWHAE\t1|0|0|0\t1\t0.25\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t2.50\t0.51\t\n-WT_EGFR\t1433T_HUMAN\tYWHAQ\t1|0|0|0\t1\t0.25\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t2.50\t0.51\t\n-WT_EGFR\tLPPRC_HUMAN\tLRPPRC\t1|3|3|3\t10\t2.50\t4\t0|0|0|0\t0.75\t1.00\t0.75\t1.00\t0.75\t2.40\t25.00\t0.00\t\n-WT_EGFR\tERRFI_HUMAN\tERRFI1\t1|2|1|1\t5\t1.25\t4\t0|0|0|0\t0.25\t0.99\t0.25\t0.99\t0.25\t2.40\t12.50\t0.28\t\n-WT_EGFR\tAP2A1_HUMAN\tAP2A1\t1|1|1|1\t4\t1.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t2.40\t10.00\t0.51\t\n-WT_EGFR\tGRB7_HUMAN\tGRB7\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tSTAT3_HUMAN\tSTAT3\t4|5|3|3\t15\t3.75\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t37.50\t0.00\t\n-WT_EGFR\tANXA2_HUMAN\tANXA2\t3|4|0|1\t8\t2.00\t4\t0|0|0|0\t0.50\t1.00\t0.50\t1.00\t0.50\t-0.11\t20.00\t0.10\t\n-WT_EGFR\tPTPRA_HUMAN\tPTPRA\t0|0|0|0\t0\t0.00\t4\t0|0|0|0\t0.00\t0.00\t0.00\t0.00\t0.00\t-0.11\t0.00\t0.51\t\n-WT_EGFR\tC1QBP_HUMAN\tC1QBP\t0|0|0|0\t0\t0.00\t4\t7|'..b'\t0|0|1|1\t0.00\t0.00\t0.00\t0.00\t0.00\t-1.55\t1.00\t0.51\t\n-ER_P85B\tPK3CA_HUMAN\tPIK3CA\t3|3|6|6\t18\t4.50\t4\t0|0|0|0\t1.00\t1.00\t1.00\t1.00\t1.00\t6.28\t45.00\t0.00\t\n-ER_P85B\tERBB3_HUMAN\tERBB3\t1|0|2|1\t4\t1.00\t4\t0|0|0|0\t0.25\t0.99\t0.25\t0.99\t0.25\t-0.11\t10.00\t0.28\t\n-ER_P85B\tADT2_HUMA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|
| b |
| diff -r 969fe96dbc7d -r 7928f149bb99 toolshed_version/tool_dependencies.xml --- a/toolshed_version/tool_dependencies.xml Tue Mar 15 16:39:22 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |