annotate filter_by_metadata.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="filter_by_metadata" name="filter_by_metadata" version="1.2.0">
 <description>Filter OTU table by removal of specified metadata</description>
 <requirements>
  <requirement type="binary">filter_by_metadata.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  filter_by_metadata.py
  --otu_table_fp=$otu_table_fp
  --map=$map
  --states=$states
  --otu_outfile=$otu_outfile
  --map_outfile=$map_outfile
  --num_seqs_per_otu=$num_seqs_per_otu
 </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="map" type="data" format="tabular" label="map"
   help="path to the map file [REQUIRED]"/>
  <param name="states" type="text"  label="states"
   help="string containing valid states, e.g. 'STUDY_NAME:DOG' [REQUIRED]"/>
  <param name="num_seqs_per_otu" type="integer" value="1" label="num_seqs_per_otu"
   help="minimum counts across samples to keep OTU, default is only to keep OTUs that are present in the samples."/>
 </inputs>
 <outputs>
  <data format="txt" name="otu_outfile"/>
  <data format="txt" name="map_outfile"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>