annotate make_prefs_file.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="make_prefs_file" name="make_prefs_file" version="1.2.1">
 <description>Generate preferences file</description>
 <requirements>
  <requirement type="binary">make_prefs_file.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  make_prefs_file.py
  --map_fname=$map_fname
  --output_fp=$output_fp
  --mapping_headers_to_use=$mapping_headers_to_use
  --background_color=$background_color
  --monte_carlo_dists=$monte_carlo_dists
  --input_taxa_file=$input_taxa_file
  --ball_scale=$ball_scale
  --arrow_line_color=$arrow_line_color
  --arrow_head_color=$arrow_head_color
 </command>
 <inputs>
  <param name="map_fname" type="data" format="tabular" label="map_fname"
   help="This is the metadata mapping file [default=('NO', 'DEFAULT')] [REQUIRED]"/>
  <param name="mapping_headers_to_use" type="data" format="tabular" label="mapping_headers_to_use"
   help="mapping fields touse in prefs file [default: ALL]"/>
  <param name="background_color" type="text" value="black" label="background_color"
   help="This is the backgroundcolor to  use in the plots. [default: black]"/>
  <param name="monte_carlo_dists" type="text" value="10" label="monte_carlo_dists"
   help="monte carlo distanceto use for each sample header [default: 10]"/>
  <param name="input_taxa_file" type="data" format="txt" label="input_taxa_file"
   help="summarized taxa file with samplecounts by taxonomy (resulting file from summarize_taxa.py)"/>
  <param name="ball_scale" type="float" value="1.0" label="ball_scale"
   help="scale factor for the size of each ball in the plots [default: 1.0]"/>
  <param name="arrow_line_color" type="text" value="white" label="arrow_line_color"
   help="arrow line color forprocrustes analysis. [default: white]"/>
  <param name="arrow_head_color" type="text" value="red" label="arrow_head_color"
   help="arrow head color forprocrustes analysis. [default: red]"/>
 </inputs>
 <outputs>
  <data format="txt" name="output_fp"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>