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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="add_taxa" name="add_taxa" version="1.2.0">
2 <description>Add taxa to OTU table</description>
3 <requirements>
4 <requirement type="binary">add_taxa.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 add_taxa.py
9 --otu_file=$otu_file
10 --taxonomy_file=$taxonomy_file
11 --output_file=$output_file
12 --id_map_file=$id_map_file
13 </command>
14 <inputs>
15 <param name="otu_file" type="data" format="txt" label="otu_file"
16 help="Path to read otu file [REQUIRED]"/>
17 <param name="taxonomy_file" type="data" format="txt" label="taxonomy_file"
18 help="Path to read taxonomy file [REQUIRED]"/>
19 <param name="id_map_file" type="data" format="tabular" label="id_map_file"
20 help="Path to read seq id to otu map file [default: ('NO', 'DEFAULT')]"/>
21 </inputs>
22 <outputs>
23 <data format="txt" name="output_file" label="${tool.name} on ${on_string}"/>
24 </outputs>
25 <tests>
26 </tests>
27 <help>
28
29 </help>
30 </tool>
31