Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/multiple_rarefactions.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="multiple_rarefactions" name="multiple_rarefactions" version="1.2.0"> | |
| 2 <description>Perform multiple subsamplings/rarefactions on an otu table</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">multiple_rarefactions.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_logfile=$output1 | |
| 9 --galaxy_outputdir=$output1.extra_files_path | |
| 10 multiple_rarefactions.py | |
| 11 --input_path=$input_path | |
| 12 --output_path=$output1.extra_files_path | |
| 13 --min=$min | |
| 14 --max=$max | |
| 15 --step=$step | |
| 16 --num-reps=$num_reps | |
| 17 $lineages_included | |
| 18 $keep_empty_otus | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param name="input_path" type="data" label="input_path" | |
| 22 help="Input otu table filepath [REQUIRED]"/> | |
| 23 <param name="min" type="integer" value="100" label="min" | |
| 24 help="Min seqs/sample [REQUIRED]"/> | |
| 25 <param name="max" type="integer" value="400" label="max" | |
| 26 help="Max seqs/sample (inclusive) [REQUIRED]"/> | |
| 27 <param name="step" type="integer" value="100" label="step" | |
| 28 help="Size of each steps between the min/max of seqs/sample (e.g. min, min+step... for every level less than or equal to max). [REQUIRED]"/> | |
| 29 <param name="num_reps" type="integer" value="10" label="num-reps" | |
| 30 help="Number of iterations at each seqs/sample level [default: 10]"/> | |
| 31 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included" | |
| 32 help="Output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/> | |
| 33 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus" | |
| 34 help="otus (rows) of all zeros are usually omitted from the output otu tables, with -k they will not be removed from the output files [default: False]"/> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Rarefied tables from $min to $max, with a step of $step"/> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 </tests> | |
| 41 <help>This tool rarefies OTU tables for use in jackknife, bootstrap, and rarefaction analyses. Samples with fewer sequences than the rarefaction depth requested for a given output otu table are omitted from those otu tables. The input is an OTU table (e.g., the output from make_otu_table). The output file is a log file listing all the rarefied otu tables produced. | |
| 42 | |
| 43 For more information, see multiple_rarefactions_ in the Qiime documentation. | |
| 44 | |
| 45 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 46 | |
| 47 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 48 | |
| 49 .. _multiple_rarefactions: http://qiime.org/scripts/multiple_rarefactions.html</help> | |
| 50 </tool> | |
| 51 |