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comparison blast_tool.xml @ 3:14894a8de3a7 draft

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author nedias
date Wed, 12 Oct 2016 18:12:18 -0400
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2:c68c3bb9cd57 3:14894a8de3a7
1 <tool id="blast_tool" name="BLAST caller for ORF" version="0.1.0">
2 <description>from given fasta polypeptide sequence</description>
3 <requirements>
4 <requirement type="package" version="1.64">biopython</requirement>
5 <requirement type="python-module">Bio</requirement>
6 </requirements>
7 <stdio>
8 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" />
10 <exit_code range=":-1" />
11 </stdio>
12 <version_command interpreter="python">blast_entry.py --version</version_command>
13 <command interpreter="python">
14 blast_entry.py -i "$input_file" -o "$output_xml" -f "$ext" -p "$program" -d "database"
15 </command>
16 <inputs>
17 <param name="input_file" type="data" label="Input File" format="fasta,fastq,sam,bam" help="FASTA, FASTQ, or SFF format." />
18 <param name="ext" type="select" value="fasta" label="Input file type">
19 <option value="fasta">Fasta</option>
20 <option value="fastq">Fastq</option>
21 <option value="sam">Sam</option>
22 <option value="bam">Bam</option>
23 </param>
24 <param name="program" type="select" value="blastp" label="BLAST program">
25 <option value="blastn">BLASTN</option>
26 <option value="blastp">BLASTP</option>
27 <option value="blastx">BLASTX</option>
28 <option value="tblastn">TBLASTN</option>
29 <option value="tblastx">TBLASTX</option>
30 </param>
31 <param name="database" type="select" value="nr" label="BLAST database">
32 <option value="nr">Nucleotide collection</option>
33 </param>
34 </inputs>
35 <outputs>
36 <data name="output_xml" format="XML" label="$input_file.name BLAST result">
37 </data>
38 </outputs>
39 </tool>