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comparison qiime/summarize_otu_by_cat.xml @ 0:003162f90751 draft

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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="summarize_otu_by_cat" name="summarize_otu_by_cat" version="2.0.0">
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 summarize_otu_by_cat.py
9 --mapping_fp=$mapping_fp
10 --otu_table_fp=$otu_table_fp
11 --mapping_category=$mapping_category
12 --output_fp=$output_fp
13 $normalize_flag
14 </command>
15 <inputs>
16 <param name="mapping_fp" type="data" format="tabular" label="input_map"
17 help="name of input map file [REQUIRED]"/>
18 <param name="otu_table_fp" type="data" format="txt" label="otu_file"
19 help="name of otu table file [REQUIRED]"/>
20 <param name="mapping_category" type="text" label="mapping_category"
21 help="name of category for OTU table [REQUIRED]"/>
22 <param name="normalize_flag" type="boolean" truevalue="--normalize_flag" falsevalue="" checked="false" label="normalize_flag"
23 help="if True will normalize counts [default: False]"/>
24 </inputs>
25 <outputs>
26 <data format="txt" name="output_fp" label="summarize_otu_by_cat"/>
27 </outputs>
28 <tests>
29 </tests>
30 <help>For more information, see summarize_otu_by_cat_ in the Qiime documentation.
31
32 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
33
34 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
35
36 .. _summarize_otu_by_cat: http://qiime.org/scripts/summarize_otu_by_cat.html</help>
37 </tool>
38