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1 <tool id="multiple_rarefactions" name="multiple_rarefactions" version="1.2.0">
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2 <description>Perform multiple subsamplings/rarefactions on an otu table</description>
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3 <requirements>
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4 <requirement type="binary">multiple_rarefactions.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_logfile=$output1
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9 --galaxy_outputdir=$output1.extra_files_path
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10 multiple_rarefactions.py
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11 --input_path=$input_path
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12 --output_path=$output1.extra_files_path
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13 --min=$min
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14 --max=$max
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15 --step=$step
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16 --num-reps=$num_reps
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17 $lineages_included
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18 $keep_empty_otus
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19 </command>
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20 <inputs>
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21 <param name="input_path" type="data" label="input_path"
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22 help="Input otu table filepath [REQUIRED]"/>
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23 <param name="min" type="integer" value="100" label="min"
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24 help="Min seqs/sample [REQUIRED]"/>
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25 <param name="max" type="integer" value="400" label="max"
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26 help="Max seqs/sample (inclusive) [REQUIRED]"/>
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27 <param name="step" type="integer" value="100" label="step"
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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]"/>
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29 <param name="num_reps" type="integer" value="10" label="num-reps"
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30 help="Number of iterations at each seqs/sample level [default: 10]"/>
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31 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
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32 help="Output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
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33 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
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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]"/>
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35 </inputs>
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36 <outputs>
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37 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Rarefied tables from $min to $max, with a step of $step"/>
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38 </outputs>
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39 <tests>
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40 </tests>
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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.
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42
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43 For more information, see multiple_rarefactions_ in the Qiime documentation.
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44
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45 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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46
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47 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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48
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49 .. _multiple_rarefactions: http://qiime.org/scripts/multiple_rarefactions.html</help>
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50 </tool>
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51
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