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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="sort_otu_table" name="sort_otu_table" version="1.2.1">
2 <description>Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file.</description>
3 <requirements>
4 <requirement type="binary">sort_otu_table.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 sort_otu_table.py
9 --input_otu_table=$input_otu_table
10 --mapping_fp=$mapping_fp
11 --sort_field=$sort_field
12 --output_fp=$output_fp
13 </command>
14 <inputs>
15 <param name="input_otu_table" type="data" format="qiimeotu" label="input_otu_table"
16 help="the input otu table [REQUIRED]"/>
17 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
18 help="the mapping file [REQUIRED]"/>
19 <param name="sort_field" type="select" label="sort_field"
20 help="field to sort by [REQUIRED]">
21 <options>
22 <filter type="data_meta" ref="mapping_fp" key="column_names" />
23 </options>
24 </param>
25 </inputs>
26 <outputs>
27 <data format="txt" name="output_fp"/>
28 </outputs>
29 <tests>
30 </tests>
31 <help>
32
33 </help>
34 </tool>
35