Mercurial > repos > nanette > nanettetest3
changeset 5:94b0fd035fec draft
Deleted selected files
| author | nanette |
|---|---|
| date | Wed, 21 Aug 2013 04:51:16 -0400 |
| parents | a99218bd868f |
| children | 066c5504de31 |
| files | test_script_path.py test_script_path.xml tool_dependencies.xml |
| diffstat | 3 files changed, 0 insertions(+), 90 deletions(-) [+] |
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--- a/test_script_path.py Wed Aug 21 04:48:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -""" -@summary: GO enrichment analysis (hotspots) -@author: nanette.coetzer@gmail.com -@version 5 - -""" -import optparse, sys -import subprocess -import tempfile -import os, re - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option("-i", "--input1", default=None, dest="input1", - help="genes") - parser.add_option("-o", "--output1", default=None, dest="output1", - help="star genes") - parser.add_option("-m", "--myflag", default=None, dest="myflag", - help="star genes") - (options, args) = parser.parse_args() - - try: - open(options.input1, "r").close() - except TypeError, e: - stop_err("You need to supply the Gene Universe file:\n" + str(e)) - except IOError, e: - stop_err("Can not open the Gene Universe file:\n" + str(e)) - - - ########################################################## - - infile = open(options.input1,"r") - inlist = [] - for line in infile: - inlist.append(line.strip()) - infile.close() - outfile = open(options.output1,"w") - for l in inlist: - outfile.write("* "+str(l)+"\n") - outfile.write(options.myflag + "\n") - outfile.close() - - ############################################## - -if __name__=="__main__": - __main__()
--- a/test_script_path.xml Wed Aug 21 04:48:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<tool id="script_path" name="nanettetest3" version="1.0.0"> - - <description>script path</description> - <requirements> - <requirement type="set_environment">SCRIPT_PATH</requirement> - </requirements> - <command interpreter="python"> - test_script_path.py --input1 $input1 --output1 $output1 --myflag \$SCRIPT_PATH - </command> - <inputs> - <param label="Gene Universe file" name="input1" type="data" format="tabular" help="A tabular file with the full set of genes from the study (gene universe)"></param> - - </inputs> - <outputs> - <data format="tabular" name="output1" /> - </outputs> - <requirements> - </requirements> - <tests> - <test> - </test> - </tests> - <help> - -**What it does** - -This tool uses the topGO R package to determine the enriched GO terms, for one or more gene lists simultaneously. - - </help> -</tool>
--- a/tool_dependencies.xml Wed Aug 21 04:48:54 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="nanettetest3" version="1.0"> - <repository changeset_revision="6c839f8050f1" name="nanettetest3" owner="nanette" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>