annotate blast_tool.xml @ 4:0145fdbdcf90 draft default tip

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<tool id="blast_tool" name="BLAST caller for ORF" version="0.1.0">
    <description>from given fasta polypeptide 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">blast_entry.py --version</version_command>
    <command interpreter="python">
blast_entry.py -i "$input_file" -o "$output_xml" -f "$ext" -p "$program" -d "database"
    </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="program" type="select" value="blastp" label="BLAST program">
	<option value="blastn">BLASTN</option>
	<option value="blastp">BLASTP</option>
	<option value="blastx">BLASTX</option>
	<option value="tblastn">TBLASTN</option>
	<option value="tblastx">TBLASTX</option>
      </param>
      <param name="database" type="select" value="nr" label="BLAST database">
	<option value="nr">Nucleotide collection</option>
      </param>
    </inputs>
    <outputs>
        <data name="output_xml" format="XML" label="$input_file.name BLAST result">
        </data>
    </outputs>
</tool>