Mercurial > repos > lucasfsilva > verjolab_tools
diff lucas_teste/lucas_teste.xml @ 0:a3e8a200e180 draft default tip
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author | lucasfsilva |
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date | Thu, 12 Mar 2015 15:57:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lucas_teste/lucas_teste.xml Thu Mar 12 15:57:13 2015 -0400 @@ -0,0 +1,111 @@ +<tool id="lucas_teste" name="lucas_teste" version="0.01"> +<description>testando o tool factory 2</description> + +<command interpreter="python"> + + lucas_teste.py --script_path "$runMe" --interpreter "python" + --tool_name "lucas_teste" + + +--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="lucas_teste"/> + + +</inputs> +<outputs> + <data format="txt" name="output1" label="${job_name}"/> + +</outputs> +<configfiles> +<configfile name="runMe"> + import sys + import os + import argparse + + argp=argparse.ArgumentParser() + argp.add_argument('--innames',default=None) + argp.add_argument('--inpaths',default=None) + argp.add_argument('--outpath',default=None) + argp.add_argument('--case_sensitive',default=0) + argp.add_argument('--additional_parameters',default=[],action="append") + argp.add_argument('otherargs', nargs=argparse.REMAINDER) + args = argp.parse_args() + + + f= open(args.outpath,'w') + if args.case_sensitive == 0: + f.write('teste:\t'.join(args.innames.split(",")).upper()) + else: + f.write('teste:\t'.join(args.innames.split(","))) + f.close() +</configfile> +</configfiles> +<tests> + + <test> + <param name="input_tab" value="dataset_1.dat,dataset_2.dat,dataset_5.dat,dataset_8.dat,dataset_13.dat,dataset_14.dat,dataset_15.dat,dataset_16.dat,dataset_17.dat,dataset_19.dat" /> + <param name="job_name" value="test1"/> + <param name="runMe" value="$runMe"/> + <output name="output1="lucas_teste_test1_output.xls" ftype="tabular"/> + + </test> + +</tests> +<help> + + +**What it Does** +nada de mais + +**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 15:46:32 +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>