Mercurial > repos > azuzolo > qiime1_3_0
view qiime/single_rarefaction.xml @ 1:2c1d19ebac20 draft default tip
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author | azuzolo |
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date | Wed, 06 Jun 2012 16:41:00 -0400 |
parents | 003162f90751 |
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<tool id="single_rarefaction" name="single_rarefaction" version="1.5.0"> <description>Perform rarefaction on an otu table</description> <requirements> <requirement type="binary">single_rarefaction.py</requirement> </requirements> <command interpreter="python"> qiime_wrapper.py single_rarefaction.py --input_path=$input_path --output_path=$output_path --depth=$depth $suppress_lineages_included $keep_empty_otus </command> <inputs> <param name="input_path" type="data" format="qiimeotutable" label="input_path" help="input otu table filepath [REQUIRED]"/> <param name="depth" type="integer" value="1" label="depth" help="sequences per sample to subsample [REQUIRED]"/> <param name="suppress_lineages_included" type="boolean" truevalue="--suppress_lineages_included" falsevalue="" checked="false" label="suppress_lineages_included" help="Exclude taxonomic (lineage) information for each OTU. Note: this will only work if lineage information is in the input OTU table. [default: False]"/> <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus" help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/> </inputs> <outputs> <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/> </outputs> <tests> </tests> <help>For more information, see single_rarefaction_ in the Qiime documentation. Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN .. _single_rarefaction: http://qiime.org/scripts/single_rarefaction.html</help> </tool>