Mercurial > repos > jjohnson > qiime

diff sort_otu_table.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/sort_otu_table.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,35 @@
+<tool id="sort_otu_table" name="sort_otu_table" version="1.2.1">
+ <description>Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file.</description>
+ <requirements>
+  <requirement type="binary">sort_otu_table.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  sort_otu_table.py
+  --input_otu_table=$input_otu_table
+  --mapping_fp=$mapping_fp
+  --sort_field=$sort_field
+  --output_fp=$output_fp
+ </command>
+ <inputs>
+  <param name="input_otu_table" type="data" format="qiimeotu"  label="input_otu_table"
+   help="the input otu table [REQUIRED]"/>
+  <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
+   help="the mapping file [REQUIRED]"/>
+  <param name="sort_field" type="select"  label="sort_field"
+   help="field to sort by [REQUIRED]">
+    <options>
+        <filter type="data_meta" ref="mapping_fp" key="column_names" />
+    </options>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="txt" name="output_fp"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+