<tool profile="16.07" id="mothur_filter_shared" name="Filter.shared" version="@WRAPPER_VERSION@.0">
    <description>remove OTUs based on various critieria</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$otu' otu.dat &&

echo 'filter.shared(
    shared=otu.dat,
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $label:
        groups=${ str($groups).replace(",","-") },
    #end if
    minabund=$minabund,
    minpercent=$minpercent,
    rarepercent=$rarepercent,
    keepties=$keepties,
    minnumsamples=$minnumsamples,
    minpercentsamples=$minpercentsamples,
    mintotal=$mintotal,
    makerare=$makerare
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" argument="shared" type="data" format="mothur.shared" label="shared - specify your shared file"/>
        <param argument="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
            <expand macro="labeloptions"/>
        </param>
        <param argument="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param argument="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU"
            help="If any samples abundance falls below the minimum, the OTU is removed"/>
        <param argument="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU"
            help="For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1.
            The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed"/>
        <param argument="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove"
            help="The OTUs chosen to be removed are the rarest.  For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance"/>
        <param argument="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true"
            label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU"
            help="For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU,
            but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10"/>
        <param argument="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU"
            help="If the number of samples present falls below the minimum, the OTU is removed"/>
        <param argument="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU"
            help="For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333,
            the minimum is 0.50, so the OTU will be removed (Default=0)"/>
        <param argument="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU"
            help="If abundance across all samples falls below the minimum, the OTU is removed"/>
        <param argument="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true"
            label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed"
            help="This will preserve the number of reads in your dataset"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="esophagus.fn.shared" ftype="mothur.shared"/>
            <output_collection name="filter_shared" count="4">
                <element name="0.03" ftype="mothur.shared">
                    <assert_contents>
                        <expand macro="test-shared-format"/>
                        <has_text text="0.03"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label and group select -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.05,0.29,0.33"/>
            <param name="groups" value="forest,pasture"/>
            <param name="minabund" value="1"/>
            <output_collection name="filter_shared" count="3">
                <element name="0.29" ftype="mothur.shared">
                    <assert_contents>
                        <expand macro="test-shared-format"/>
                        <has_text text="0.29"/>
                    </assert_contents>
                </element>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The filter.shared_ is used to remove OTUs based on various critieria.

.. _filter.shared: https://www.mothur.org/wiki/Filter.shared

    ]]></help>
    <citations>
        <citation type="doi">10.1128/AEM.01541-09</citation>
    </citations>
</tool>