view filter_otu_table.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="filter_otu_table" name="filter_otu_table" version="1.2.0">
 <description>Filters OTU table by minimum OTU count and number of samples or by taxonomy</description>
 <requirements>
  <requirement type="binary">filter_otu_table.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  filter_otu_table.py
  --otu_table_fp=$otu_table_fp
  --min_count=$min_count
  --min_samples=$min_samples
  --include_taxonomy=$include_taxonomy
  --exclude_taxonomy=$exclude_taxonomy
  --dir_path=$dir_path
  --seqs_per_sample=$seqs_per_sample
 </command>
 <inputs>
  <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
   help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
  <param name="min_count" type="integer" value="1" label="min_count"
   help="retain OTUs with at least this many sequences [default=1]"/>
  <param name="min_samples" type="integer" value="2" label="min_samples"
   help="retain OTUs found in at least this many samples [default=2]"/>
  <param name="include_taxonomy" type="text" value="" label="include_taxonomy"
   help="list of taxonomy terms to include [default=]"/>
  <param name="exclude_taxonomy" type="text" value="" label="exclude_taxonomy"
   help="list of taxonomy terms to exclude [default=]"/>
  <param name="dir_path" type="text" value="./" label="dir_path"
   help="directory prefix for all analyses [default=./]"/>
  <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
   help="minimum sequences per sample to retain the sample. [default=('NO', 'DEFAULT')]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>