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1 <tool id="blast_tool" name="BLAST caller for ORF" version="0.1.0">
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2 <description>from given fasta polypeptide sequence</description>
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3 <requirements>
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4 <requirement type="package" version="1.64">biopython</requirement>
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5 <requirement type="python-module">Bio</requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 </stdio>
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12 <version_command interpreter="python">blast_entry.py --version</version_command>
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13 <command interpreter="python">
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14 blast_entry.py -i "$input_file" -o "$output_xml" -f "$ext" -p "$program" -d "database"
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15 </command>
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16 <inputs>
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17 <param name="input_file" type="data" label="Input File" format="fasta,fastq,sam,bam" help="FASTA, FASTQ, or SFF format." />
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18 <param name="ext" type="select" value="fasta" label="Input file type">
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19 <option value="fasta">Fasta</option>
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20 <option value="fastq">Fastq</option>
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21 <option value="sam">Sam</option>
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22 <option value="bam">Bam</option>
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23 </param>
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24 <param name="program" type="select" value="blastp" label="BLAST program">
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25 <option value="blastn">BLASTN</option>
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26 <option value="blastp">BLASTP</option>
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27 <option value="blastx">BLASTX</option>
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28 <option value="tblastn">TBLASTN</option>
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29 <option value="tblastx">TBLASTX</option>
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30 </param>
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31 <param name="database" type="select" value="nr" label="BLAST database">
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32 <option value="nr">Nucleotide collection</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="output_xml" format="XML" label="$input_file.name BLAST result">
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37 </data>
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38 </outputs>
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39 </tool>
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