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1 <tool id="single_rarefaction" name="single_rarefaction" version="1.5.0">
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2 <description>Perform rarefaction on an otu table</description>
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3 <requirements>
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4 <requirement type="binary">single_rarefaction.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 single_rarefaction.py
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9 --input_path=$input_path
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10 --output_path=$output_path
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11 --depth=$depth
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12 $suppress_lineages_included
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13 $keep_empty_otus
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14 </command>
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15 <inputs>
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16 <param name="input_path" type="data" format="qiimeotutable" label="input_path"
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17 help="input otu table filepath [REQUIRED]"/>
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18 <param name="depth" type="integer" value="1" label="depth"
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19 help="sequences per sample to subsample [REQUIRED]"/>
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20 <param name="suppress_lineages_included" type="boolean" truevalue="--suppress_lineages_included" falsevalue="" checked="false" label="suppress_lineages_included"
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21 help="Exclude taxonomic (lineage) information for each OTU. Note: this will only work if lineage information is in the input OTU table. [default: False]"/>
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22 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
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23 help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/>
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24 </inputs>
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25 <outputs>
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26 <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/>
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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 single_rarefaction_ in the Qiime documentation.
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31
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32 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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33
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34 .. _single_rarefaction: http://qiime.org/scripts/single_rarefaction.html</help>
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35 </tool>
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36
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