diff trim_sff_primers.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trim_sff_primers.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,40 @@
+<tool id="trim_sff_primers" name="trim_sff_primers" version="1.2.0">
+ <description>Trim sff primers</description>
+ <requirements>
+  <requirement type="binary">trim_sff_primers.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  trim_sff_primers.py
+  --libdir=$libdir
+  --input_map=$input_map
+  --sfffile_path=$sfffile_path
+  --sffinfo_path=$sffinfo_path
+  $use_sfftools
+  $debug
+ </command>
+ <inputs>
+  <param name="libdir" type="text"  label="libdir"
+   help="The directory containing per-library sff files [REQUIRED]"/>
+  <param name="input_map" type="data" format="tabular" label="input_map"
+   help="Path to the input mapping file describing the libraries [REQUIRED]"/>
+  <param name="sfffile_path" type="text" value="sfffile" label="sfffile_path"
+   help="Path to sfffile binary [default: sfffile]"/>
+  <param name="sffinfo_path" type="text" value="sffinfo" label="sffinfo_path"
+   help="Path to sffinfo binary [default: sffinfo]"/>
+  <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
+   help="Use external sffinfo and sfffile programs instead of equivalent Python implementation."/>
+  <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="debug"
+   help="Print command-line output for debugging [default: False]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+