<tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.1.0">
    <description>Extract a single sequence from a fasta file.</description>
     <requirements>
        <requirement type="package" version="1.6.924">perl-bioperl</requirement>
    </requirements>
    <command >
        perl $__tool_directory__/fa-extract-few.pl
        -f $dataset
	$exact
        $inverse
        #if $file_or_type.select == "list"
          --list $file_or_type.list_file
        #else
          $file_or_type.id
        #end if

        > 
        $output
    </command>
    <inputs>
        <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
        <param name="exact" type="boolean" truevalue="--exact" label="Exact matches only" help="Will only match exact matches for fasta id"/>
        <param name="inverse" type="boolean" truevalue="--inverse" label="Entries NOT matching" help="Will return the sequences not matching the given ids"/>

        <conditional name="file_or_type">
          <param name="select" type="select" label="List file or single pattern">
            <option value="list">List file</option>
            <option value="single">Single Pattern</option>
          </param>
          <when value="list">
            <param name="list_file" type="data" format="txt" help="List of pattern to find." label="List file"/>
          </when>
          <when value="single">
            <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." />
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/>
    </outputs>
    <tests>
      <test>
        <param name="dataset" value="input.fasta"/>
        <param name="select" value="single"/>
        <param name="id" value="B0R37_29930"/>
        <output name="output" value="output.fasta"/>
      </test>
    </tests>
    <help>
**Fasta Extract Sequence**
Extracts a fasta sequence from a multfasta by id (exact or partial)

Latest author:
Written by Philip Mabon   - Public Health Agency of Canada

Original authors:
Written by Torsten Seemann - Victorian Bioinformatics Consortium

Wrapped by Simon Gladman - Victorian Bioinformatics Consortium


------

Outputs in fasta format.
    
------

Inputs:

Fasta dataset

Sequence id
    </help>
    <citations>
    </citations>
</tool>