Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/single_rarefaction.xml @ 0:003162f90751 draft
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| author | azuzolo |
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| date | Wed, 06 Jun 2012 16:40:30 -0400 |
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| -1:000000000000 | 0:003162f90751 |
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| 1 <tool id="single_rarefaction" name="single_rarefaction" version="1.5.0"> | |
| 2 <description>Perform rarefaction on an otu table</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">single_rarefaction.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 single_rarefaction.py | |
| 9 --input_path=$input_path | |
| 10 --output_path=$output_path | |
| 11 --depth=$depth | |
| 12 $suppress_lineages_included | |
| 13 $keep_empty_otus | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param name="input_path" type="data" format="qiimeotutable" label="input_path" | |
| 17 help="input otu table filepath [REQUIRED]"/> | |
| 18 <param name="depth" type="integer" value="1" label="depth" | |
| 19 help="sequences per sample to subsample [REQUIRED]"/> | |
| 20 <param name="suppress_lineages_included" type="boolean" truevalue="--suppress_lineages_included" falsevalue="" checked="false" label="suppress_lineages_included" | |
| 21 help="Exclude taxonomic (lineage) information for each OTU. Note: this will only work if lineage information is in the input OTU table. [default: False]"/> | |
| 22 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus" | |
| 23 help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 </tests> | |
| 30 <help>For more information, see single_rarefaction_ in the Qiime documentation. | |
| 31 | |
| 32 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 33 | |
| 34 .. _single_rarefaction: http://qiime.org/scripts/single_rarefaction.html</help> | |
| 35 </tool> | |
| 36 |