--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/process_sff.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,35 @@
+<tool id="process_sff" name="process_sff" version="1.2.0">
+ <description>Convert sff to FASTA and QUAL files</description>
+ <requirements>
+  <requirement type="binary">process_sff.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  process_sff.py
+  --input_dir=$input_dir
+  $make_flowgram
+  $convert_to_FLX
+  $use_sfftools
+  --output_dir=$__new_file_path__
+ </command>
+ <inputs>
+  <param name="input_dir" type="text"  label="input_dir"
+   help="Input directory of sff files [REQUIRED]"/>
+  <param name="make_flowgram" type="boolean" truevalue="--make_flowgram" falsevalue="" checked="false" label="make_flowgram"
+   help="generate a flowgram file. [default: False]"/>
+  <param name="convert_to_FLX" type="boolean" truevalue="--convert_to_FLX" falsevalue="" checked="false" label="convert_to_FLX"
+   help="convert Titanium reads to FLX length. [default: False]"/>
+  <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
+   help="use the external programs sfffile and sffinfo for processing, instead of the equivalent python implementation"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+