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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="blast_wrapper" name="blast_wrapper" version="1.2.0">
2 <description>Blast Interface</description>
3 <requirements>
4 <requirement type="binary">blast_wrapper.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 blast_wrapper.py
10 --input_fasta_fp=$input_fasta_fp
11 --refseqs_fp=$refseqs_fp
12 --num_seqs_per_blast_run=$num_seqs_per_blast_run
13 </command>
14 <inputs>
15 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
16 help="path to the input fasta file [REQUIRED]"/>
17 <param name="refseqs_fp" type="data" format="fasta" label="refseqs_fp"
18 help="path to blast database as a fasta file [REQUIRED]"/>
19 <param name="num_seqs_per_blast_run" type="integer" value="1000" label="num_seqs_per_blast_run"
20 help="number of sequences passed to each blast call - useful for very large sequence collections [default: 1000]"/>
21 </inputs>
22 <outputs>
23
24 </outputs>
25 <tests>
26 </tests>
27 <help>
28
29 </help>
30 </tool>
31