view orf_tool.xml @ 7:0eda2c588bcd draft

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<tool id="orf_tool" name="Open Reading Frame Extract Tool" version="0.1.0">
    <description>from given fasta RNA sequence</description>
    <requirements>
        <requirement type="package" version="1.64">biopython</requirement>
        <requirement type="python-module">Bio</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">entry.py --version</version_command>
    <command interpreter="python">
entry.py -i "$input_file" -a "$output_all" -d "$output_dest" -f "$ext" -l "$length"
    </command>
    <inputs>
      <param name="input_file" type="data" label="Input File" format="fasta,fastq,sam,bam" help="FASTA, FASTQ, or SFF format." />
      <param name="ext" type="select" value="fasta" label="Input file type">
	<option value="fasta">Fasta</option>
	<option value="fastq">Fastq</option>
	<option value="sam">Sam</option>
	<option value="bam">Bam</option>
      </param>
      <param name="length" type="integer" value="100" max="100" min="1"  label="Length" help="Percentage of the max match." />
    </inputs>
    <outputs>
        <data name="output_all" format_source="input_file" metadata_source="input_file" label="$input_file.name all matches">
        </data>
        <data name="output_dest" format_source="input_file" metadata_source="input_file" label="$input_file.name designated matches">
        </data>
    </outputs>
</tool>