Mercurial > repos > jjohnson > qiime

diff adjust_seq_orientation.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/adjust_seq_orientation.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,29 @@
+<tool id="adjust_seq_orientation" name="adjust_seq_orientation" version="1.2.0">
+ <description>Get the reverse complement of all sequences</description>
+ <requirements>
+  <requirement type="binary">adjust_seq_orientation.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  adjust_seq_orientation.py
+  --input_fasta_fp=$input_fasta_fp
+  --output_fp=$output_fp
+  $retain_seq_id
+ </command>
+ <inputs>
+  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp"
+   help="path to the input fasta file [REQUIRED]"/>
+  <param name="retain_seq_id" type="boolean" truevalue="--retain_seq_id" falsevalue="" checked="false" label="retain_seq_id"
+   help="leave seq description lines untouched [default: append ' RC' to seq description lines]"/>
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fp" label="${tool.name} on ${on_string}: (RC)"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+