Mercurial > repos > jjohnson > qiime

diff blast_wrapper.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
author: Jim Johnson <jj@umn.edu>
date: Sun, 17 Jul 2011 10:30:11 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_wrapper.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,31 @@
+<tool id="blast_wrapper" name="blast_wrapper" version="1.2.0">
+ <description>Blast Interface</description>
+ <requirements>
+  <requirement type="binary">blast_wrapper.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  blast_wrapper.py
+  --input_fasta_fp=$input_fasta_fp
+  --refseqs_fp=$refseqs_fp
+  --num_seqs_per_blast_run=$num_seqs_per_blast_run
+ </command>
+ <inputs>
+  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
+   help="path to the input fasta file [REQUIRED]"/>
+  <param name="refseqs_fp" type="data" format="fasta" label="refseqs_fp"
+   help="path to blast database as a fasta file [REQUIRED]"/>
+  <param name="num_seqs_per_blast_run" type="integer" value="1000" label="num_seqs_per_blast_run"
+   help="number of sequences passed to each blast call - useful for very large sequence collections [default: 1000]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+