Mercurial > repos > jjohnson > qiime
view trim_sff_primers.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Sun, 17 Jul 2011 10:30:11 -0500 |
parents | |
children |
line wrap: on
line source
<tool id="trim_sff_primers" name="trim_sff_primers" version="1.2.0"> <description>Trim sff primers</description> <requirements> <requirement type="binary">trim_sff_primers.py</requirement> </requirements> <command interpreter="python"> qiime_wrapper.py --galaxy_tmpdir='$__new_file_path__' trim_sff_primers.py --libdir=$libdir --input_map=$input_map --sfffile_path=$sfffile_path --sffinfo_path=$sffinfo_path $use_sfftools $debug </command> <inputs> <param name="libdir" type="text" label="libdir" help="The directory containing per-library sff files [REQUIRED]"/> <param name="input_map" type="data" format="tabular" label="input_map" help="Path to the input mapping file describing the libraries [REQUIRED]"/> <param name="sfffile_path" type="text" value="sfffile" label="sfffile_path" help="Path to sfffile binary [default: sfffile]"/> <param name="sffinfo_path" type="text" value="sffinfo" label="sffinfo_path" help="Path to sffinfo binary [default: sffinfo]"/> <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools" help="Use external sffinfo and sfffile programs instead of equivalent Python implementation."/> <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="debug" help="Print command-line output for debugging [default: False]"/> </inputs> <outputs> </outputs> <tests> </tests> <help> </help> </tool>