view filter_fasta.xml @ 13:55990dea42fb draft

Uploaded

<tool id="filter_fasta" name="Filter FASTA">
  <description></description>
  <command interpreter="python">filter_fasta.py $fasta_input $scaf_input $fasta_output</command>
  <inputs>
    <param format="fasta" name="fasta_input" type="data" label="FASTA Database"/>
    <param format="txt" name="scaf_input" type="data" label="Scaffold Report"/>
  </inputs>
  <outputs>
    <data format="fasta" name="fasta_output" label="Filtered FASTA"/>    
  </outputs>
  <stdio>
    <regex match="Error|error"
     source="stdout"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error|error"
     source="stderr"
           level="fatal"
           description="Unknown error"/>
    <regex match="Error: bad bait"
           source="stdout"
           level="fatal"
           description="Error: bad bait"/>
  </stdio> 
  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
  <help>
This program will filter a fasta file using a data file containing an "Accession" or "Accession Number" column.

**Required input:**
1) fasta file to be filtered
2) data file containing a "Accession" or "Accession Number" column
  </help>
</tool>