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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="summarize_otu_by_cat" name="summarize_otu_by_cat" version="1.2.0">
2 <description>Create a summarized OTU table for a specific metadata category</description>
3 <requirements>
4 <requirement type="binary">summarize_otu_by_cat.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 summarize_otu_by_cat.py
10 --input_map=$input_map
11 --otu_file=$otu_file
12 --meta_category=$meta_category
13 --dir-prefix=$dir_prefix
14 $normalize_flag
15 </command>
16 <inputs>
17 <param name="input_map" type="data" format="tabular" label="input_map"
18 help="name of input map file [REQUIRED]"/>
19 <param name="otu_file" type="data" format="txt" label="otu_file"
20 help="name of otu table file [REQUIRED]"/>
21 <param name="meta_category" type="text" label="meta_category"
22 help="name of category for OTU table [REQUIRED]"/>
23 <param name="dir_prefix" type="text" label="dir-prefix"
24 help="directory prefix for all analyses [default: cwd]"/>
25 <param name="normalize_flag" type="boolean" truevalue="--normalize_flag" falsevalue="" checked="false" label="normalize_flag"
26 help="if True will normalize counts [default: False]"/>
27 </inputs>
28 <outputs>
29
30 </outputs>
31 <tests>
32 </tests>
33 <help>
34
35 </help>
36 </tool>
37