view filter_otus_by_sample.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="filter_otus_by_sample" name="filter_otus_by_sample" version="1.2.0">
 <description>Filter OTU mapping file and sequences by SampleIDs</description>
 <requirements>
  <requirement type="binary">filter_otus_by_sample.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  filter_otus_by_sample.py
  --otu_map_fp=$otu_map_fp
  --input_fasta_fp=$input_fasta_fp
  --samples_to_extract=$samples_to_extract
  --output_dir=$__new_file_path__
 </command>
 <inputs>
  <param name="otu_map_fp" type="data" format="tabular" label="otu_map_fp"
   help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/>
  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
   help="path to the input fasta file [REQUIRED]"/>
  <param name="samples_to_extract" type="text"  label="samples_to_extract"
   help="This is a list of sample ids, which should be removed from the OTU file [REQUIRED]"/>
 </inputs>
 <outputs>
  
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>