view trim_sff_primers.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<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>