<tool id="qiime_multiple_rarefactions" name="Perform multiple subsamplings/rarefactions" version="1.9.1">
    <description>on an otu table</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <command>
<![CDATA[
    multiple_rarefactions.py -i $input_path -o multiple_rarefactions_output -m $min -x $max -s $step

    #if $numreps:
     -n $numreps
    #end if

    #if $lineages_included:
     --lineages_included
    #end if

    #if $keep_empty_otus:
     -k
    #end if

    #if $subsample_multinomial:
     --subsample_multinomial
    #end if
]]>
    </command>

    <inputs>
        <param label="-i/--input_path: Input OTU table filepath." 
            name="input_path" optional="False" type="data"/>
        <param label="-m/--min: Minimum number of seqs/sample for rarefaction." 
            name="min" optional="False" type="integer" value="0"/>
        <param label="-x/--max: Maximum number of seqs/sample (inclusive) for r
            arefaction. " name="max" optional="False" type="integer" value="0"/>
        <param label="-s/--step: Size of each steps between the min/max of 
            seqs/sample (e.g. min, min+step... for level = max)." name="step" 
            optional="False" type="integer" value="0"/>
        <param default="10" label="-n/--num-reps: The number of iterations at 
            each step. [default: 10]" name="numreps" optional="True" type="integer"/>
        <param label="--lineages_included: Retain taxonomic (lineage) information 
            for each OTU. Note: this will only work if lineage information is in 
            the input OTU table. [default: False]" name="lineages_included" 
            selected="False" type="boolean"/>
        <param label="-k/--keep_empty_otus: Retain OTUs of all zeros, which are 
            usually omitted from the output OTU tables. [default: False]" 
            name="keep_empty_otus" selected="False" type="boolean"/>
        <param label="--subsample_multinomial: subsample using subsampling with 
            replacement [default: False]" name="subsample_multinomial" 
            selected="False" type="boolean"/>
    </inputs>

    <outputs>
        <data format="tgz" name="multiple_rarefactions" label="Multiple_rarefaction.tgz" />
        <data format="tgz" name="output_dir" label="Alpha diversity.tgz" />
        <data format="text" name="alpha_param" label="alpha_param.txt"  />
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <help><![CDATA[
To perform bootstrap, jackknife, and rarefaction analyses, the otu table must be subsampled (rarefied). This script rarefies, or subsamples, OTU tables. This does not provide curves of diversity by number of sequences in a sample. Rather it creates a series of subsampled OTU tables by random sampling (without replacement) of the input OTU table. Samples that have fewer sequences then the requested rarefaction depth for a given output otu table are omitted from those ouput otu tables. The pseudo-random number generator used for rarefaction by subsampling is NumPy’s default - an implementation of the Mersenne twister PRNG.
    ]]>
    </help>

    <citations>
        <expand macro="citations" />
    </citations>
</tool>