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changeset 25:f6f472d55b35 draft

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Deleted selected files
author bornea
date Tue, 12 Jan 2016 16:23:56 -0500
parents 7cd627b3d184
children bb1601260366
files SAINTexpress_v3.6.1__2015-05-03.zip saint_wrapper.py saint_wrapper.xml tool_dependencies.xml
diffstat 4 files changed, 0 insertions(+), 105 deletions(-) [+]
line wrap: on
line diff
Binary file SAINTexpress_v3.6.1__2015-05-03.zip has changed
--- a/saint_wrapper.py	Tue Nov 17 13:35:02 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-import os
-import sys
-
-inter_file = sys.argv[1]
-prey_file = sys.argv[2]
-bait_file = sys.argv[3]
-num_of_rep = sys.argv[4]
-vc_bool = sys.argv[5]
-vc_num = sys.argv[6]
-go_bool = sys.argv[7]
-go_file = sys.argv[8]
-output_file = sys.argv[9]
-ins_path = sys.argv[10]
-
-def first_run_check():
-	os.chdir(ins_path)
-	dirs_list = []
-	for (dirpath, dirnames, filename) in os.walk("./"):
-		dirs_list.extend(dirnames)
-		break
-	if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
-		pass
-	else: 
-		cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip"
-		os.system(cmd)
-		os.chdir("./SAINTexpress_v3.6.1__2015-05-03")
-		cmd1 = r"make -j"
-		os.system(cmd1)
-
-def default_run(inter_file1,prey_file1,bait_file1,output_file1,num_of_rep1):
-	cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) 
-	os.system(cmd) 
-	open('list.txt')
-	os.rename('list.txt', str(output_file1)) 
-
-def with_L(inter_file1,prey_file1,bait_file1,output_file1,vc_num1,num_of_rep1):
-	cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) 
-	os.system(cmd) 
-	open('list.txt')
-	os.rename('list.txt', str(output_file1)) 
-
-def external_data_no_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1):
-	cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1)
-	os.system(cmd) 
-	open('list.txt')
-	os.rename('list.txt', str(output_file1)) 
-
-def external_data_with_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1,vc_num1):
-	cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1)
-	os.system(cmd) 
-	open('list.txt')
-	os.rename('list.txt', str(output_file1)) 
-
-first_run_check()
-if (vc_bool == "true"):
-	if (go_bool == "false"):
-		with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
-	elif (go_bool == "true"):
-		external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
-elif (vc_bool == "false"):
-	if (go_bool == "false"):
-		default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
-	elif (go_bool == "true"):
-		external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)
--- a/saint_wrapper.xml	Tue Nov 17 13:35:02 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<tool id="saint_wrapper" name="SAINT">
-  <description></description>
-  <command interpreter="python">saint_wrapper.py $inter_input $prey_input $bait_input $rep_num $vc_bool $vc_num $go_bool $go_file $output \$INSTALL_RUN_PATH/</command>
-  <requirements>
-    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
-  </requirements>
-  <inputs>
-    <param format="txt" name="inter_input" type="data" label="Interactions File"/>
-    <param format="txt" name="prey_input" type="data" label="Prey File"/>
-    <param format="txt" name="bait_input" type="data" label="Bait File"/>
-    <param name="rep_num" type="integer" value="100" label="Number of Replicates" help="the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait.  This option is useful when some baits have more replicates than others." />
-    <param type="boolean" name="vc_bool" checked="false" label="Using Virtual Control Purifications by Compression"/>
-    <param name="vc_num" type="integer" value="1" label="Number of Virtual Controls" />
-    <param type="boolean" name="go_bool" checked="false" label="Incorporate External Data Sources" />
-    <param format="txt" name="go_file" type="data" optional="true" label="External Data File" help="SAINT can be run with the known interaction data in hand and it will incorporate the number of observed interactions into the statistics to boost identification probability."/>
-  </inputs>
-  <outputs>
-    <data format="txt" name="output" />
-  </outputs>
-  <stdio>
-    <regex match="error"
-	   source="stdout"
-           level="fatal"
-           description="Unknown error"/>
-  </stdio> 
-
-  <tests>
-    <test>
-      <param name="input" value="fa_gc_content_input.fa"/>
-      <output name="out_file1" file="fa_gc_content_output.txt"/>
-    </test>
-  </tests>
-  <help>
-  </help>
-</tool>
--- a/tool_dependencies.xml	Tue Nov 17 13:35:02 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="INSTALL_RUN_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
-    </set_environment>-->
-</tool_dependency>
\ No newline at end of file