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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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e5c3175506b7 Initial tool configs for qiime, most need work.
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1 <tool id="summarize_otu_by_cat" name="summarize_otu_by_cat" version="1.2.0">
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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 --galaxy_tmpdir='$__new_file_path__'
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9 summarize_otu_by_cat.py
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10 --input_map=$input_map
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11 --otu_file=$otu_file
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12 --meta_category=$meta_category
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13 --dir-prefix=$dir_prefix
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14 $normalize_flag
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15 </command>
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16 <inputs>
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17 <param name="input_map" type="data" format="tabular" label="input_map"
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18 help="name of input map file [REQUIRED]"/>
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19 <param name="otu_file" type="data" format="txt" label="otu_file"
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20 help="name of otu table file [REQUIRED]"/>
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21 <param name="meta_category" type="text" label="meta_category"
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22 help="name of category for OTU table [REQUIRED]"/>
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23 <param name="dir_prefix" type="text" label="dir-prefix"
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24 help="directory prefix for all analyses [default: cwd]"/>
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25 <param name="normalize_flag" type="boolean" truevalue="--normalize_flag" falsevalue="" checked="false" label="normalize_flag"
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26 help="if True will normalize counts [default: False]"/>
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27 </inputs>
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28 <outputs>
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30 </outputs>
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31 <tests>
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32 </tests>
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33 <help>
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34
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35 </help>
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36 </tool>
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