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