view filter_fasta.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="filter_fasta" name="filter_fasta" version="1.2.0">
 <description>This script can be applied to remove sequences from a fasta file based on input criteria.</description>
 <requirements>
  <requirement type="binary">filter_fasta.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  filter_fasta.py
  --input_fasta_fp=$input_fasta_fp
  --output_fasta_fp=$output_fasta_fp
  --otu_map=$otu_map
  --seq_id_fp=$seq_id_fp
  --subject_fasta_fp=$subject_fasta_fp
  --seq_id_prefix=$seq_id_prefix
  $negate
 </command>
 <inputs>
  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
   help="path to the input fasta file [REQUIRED]"/>
  <param name="otu_map" type="data" format="tabular" label="otu_map"
   help="an OTU map where sequences ids are those which should be retained"/>
  <param name="seq_id_fp" type="data" format="txt" label="seq_id_fp"
   help="A list of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/>
  <param name="subject_fasta_fp" type="data" format="fasta" label="subject_fasta_fp"
   help="A fasta file where the seq ids should be retained."/>
  <param name="seq_id_prefix" type="text"  label="seq_id_prefix"
   help="keep seqs where seq_id starts with this prefix"/>
  <param name="negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="negate"
   help="discard passed seq ids rather than keep passed seq ids [default: False]"/>
 </inputs>
 <outputs>
  <data format="txt" name="output_fasta_fp"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>