Mercurial > repos > lucasfsilva > verjo3_teste
view teste_out/teste_out.xml @ 0:a3d3dc004a88 draft default tip
Uploaded
author | lucasfsilva |
---|---|
date | Thu, 12 Mar 2015 16:36:22 -0400 |
parents | |
children |
line wrap: on
line source
<tool id="teste_out" name="teste_out" version="0.01"> <description>teste_tools_lucas</description> <command interpreter="python"> teste_out.py --script_path "$runMe" --interpreter "python" --tool_name "teste_out" --input_formats None #for intab in $input1: --input_tab "${intab},${intab.name}" #end for --output_dir "./" --output_tab "$output1" </command> <inputs> <param name="input_tab" multiple="true" type="data" format="None" label="Select one or more None input files from your history" help="Multiple inputs may be selected assuming the script can deal with them..."/> <param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="teste_out"/> </inputs> <outputs> <data format="txt" name="output1" label="${job_name}"/> </outputs> <configfiles> <configfile name="runMe"> import sys import os import argparse argp=argparse.ArgumentParser() argp.add_argument('--innames',default=None) argp.add_argument('--inpaths',default=None) argp.add_argument('--outpath',default=None) argp.add_argument('--case_sensitive',default=0) argp.add_argument('--additional_parameters',default=[],action="append") argp.add_argument('otherargs', nargs=argparse.REMAINDER) args = argp.parse_args() f= open(args.outpath,'w') if args.case_sensitive == 0: f.write('teste:\t'.join(args.innames.split(",")).upper()) else: f.write('teste:\t'.join(args.innames.split(","))) f.close() </configfile> </configfiles> <tests> <test> <param name="input_tab" value="dataset_20.dat,dataset_22.dat" /> <param name="job_name" value="test1"/> <param name="runMe" value="$runMe"/> <output name="output1="teste_out_test1_output.xls" ftype="tabular"/> </test> </tests> <help> **What it Does** teste **Script** Pressing execute will run the following code over your input file and generate some outputs in your history:: import sys import os import argparse argp=argparse.ArgumentParser() argp.add_argument('--innames',default=None) argp.add_argument('--inpaths',default=None) argp.add_argument('--outpath',default=None) argp.add_argument('--case_sensitive',default=0) argp.add_argument('--additional_parameters',default=[],action="append") argp.add_argument('otherargs', nargs=argparse.REMAINDER) args = argp.parse_args() f= open(args.outpath,'w') if args.case_sensitive == 0: f.write('teste:\t'.join(args.innames.split(",")).upper()) else: f.write('teste:\t'.join(args.innames.split(","))) f.close() **Attribution** This Galaxy tool was created by bioinfolucas@gmail.com at 12/03/2015 17:34:22 using the Galaxy Tool Factory. See https://bitbucket.org/fubar/galaxytoolfactory for details of that project Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573 This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2 https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2 </help> <citations> <citation type="doi">10.1093/bioinformatics/bts573</citation> </citations> </tool>