comparison multiple_rarefactions.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

0:e5c3175506b7

<tool id="multiple_rarefactions" name="multiple_rarefactions" version="1.2.0">
 <description>Perform multiple subsamplings/rarefactions on an otu table</description>
 <requirements>
  <requirement type="binary">multiple_rarefactions.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  multiple_rarefactions.py
  --input_path=$input_path
  --output_path=$output_path
  --min=$min
  --max=$max
  --step=$step
  --num-reps=$num_reps
  $lineages_included
  $keep_empty_otus
 </command>
 <inputs>
  <param name="input_path" type="text"  label="input_path"
   help="input otu table filepath [REQUIRED]"/>
  <param name="min" type="integer" value="-1" label="min"
   help="min seqs/sample [REQUIRED]"/>
  <param name="max" type="integer" value="-1" label="max"
   help="max seqs/sample (inclusive) [REQUIRED]"/>
  <param name="step" type="integer" value="-1" label="step"
   help="levels: min, min+step... for level {= max [REQUIRED]"/>
  <param name="num_reps" type="integer" value="1" label="num-reps"
   help="num iterations at each seqs/sample level [default: 1]"/>
  <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
   help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
  <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
   help="otus (rows) of all zeros are usually omitted from the output otu tables, with -k they will not be removed from the output files [default: False]"/>
 </inputs>
 <outputs>
  <data format="txt" name="output_path"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>