| Previous changeset 24:7cd627b3d184 (2015-11-17) Next changeset 26:bb1601260366 (2016-01-28) |
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Commit message:
Deleted selected files |
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removed:
SAINTexpress_v3.6.1__2015-05-03.zip saint_wrapper.py saint_wrapper.xml tool_dependencies.xml |
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| diff -r 7cd627b3d184 -r f6f472d55b35 SAINTexpress_v3.6.1__2015-05-03.zip |
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| Binary file SAINTexpress_v3.6.1__2015-05-03.zip has changed |
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| diff -r 7cd627b3d184 -r f6f472d55b35 saint_wrapper.py --- a/saint_wrapper.py Tue Nov 17 13:35:02 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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) |
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| diff -r 7cd627b3d184 -r f6f472d55b35 saint_wrapper.xml --- a/saint_wrapper.xml Tue Nov 17 13:35:02 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r 7cd627b3d184 -r f6f472d55b35 tool_dependencies.xml --- a/tool_dependencies.xml Tue Nov 17 13:35:02 2015 -0500 +++ /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 |