diff summarize_otu_by_cat.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_otu_by_cat.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,37 @@
+<tool id="summarize_otu_by_cat" name="summarize_otu_by_cat" version="1.2.0">
+ <description>Create a summarized OTU table for a specific metadata category</description>
+ <requirements>
+  <requirement type="binary">summarize_otu_by_cat.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  summarize_otu_by_cat.py
+  --input_map=$input_map
+  --otu_file=$otu_file
+  --meta_category=$meta_category
+  --dir-prefix=$dir_prefix
+  $normalize_flag
+ </command>
+ <inputs>
+  <param name="input_map" type="data" format="tabular" label="input_map"
+   help="name of input map file [REQUIRED]"/>
+  <param name="otu_file" type="data" format="txt" label="otu_file"
+   help="name of otu table file [REQUIRED]"/>
+  <param name="meta_category" type="text"  label="meta_category"
+   help="name of category for OTU table [REQUIRED]"/>
+  <param name="dir_prefix" type="text"  label="dir-prefix"
+   help="directory prefix for all analyses [default: cwd]"/>
+  <param name="normalize_flag" type="boolean" truevalue="--normalize_flag" falsevalue="" checked="false" label="normalize_flag"
+   help="if True will normalize counts [default: False]"/>
+ </inputs>
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+