<tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
    <description>Removes OTUs from various file formats</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

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

echo 'remove.otus(
    #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
        constaxonomy=infile.otu.data,
    #end if
    #if $infile.otu.is_of_type("mothur.otu.corr"):
        otucorr=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.axes"):
        corraxes=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.list"):
        list=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.shared"):
        shared=infile.otu.dat,
    #end if
    #if $infile.intype == "in_shared" and $infile.label:
        label=${ str($infile.label).replace(",","-") },
    #end if
    accnos=accnos.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
        <conditional name="infile">
            <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
                <option value="in_shared">Shared or List file</option>
                <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
            </param>
            <when value="in_shared">
                <param name="otu" type="data" format="mothur.list,mothur.shared" label="shared/list - allows you to input a list file you wish to select OTUs from. "/>
                <param name="label" type="select" label="label - pick (one) OTU Label" optional="true" help="By default first label in your file is used">
                    <expand macro="labeloptions"/>
                </param>
            </when>
            <when value="in_other">
                <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
            </when>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
    </outputs>
    <tests>
        <test><!-- test with shared/list input and label selection -->
            <param name="accnos" value="amazon.accnos.otulabels"/>
            <param name="intype" value="in_shared"/>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="label" value="0.22"/>
            <output name="pick_out" ftype="mothur.list">
                <assert_contents>
                    <expand macro="test-list-format"/>
                    <has_text text="U68686"/>
                    <has_text text="0.22"/>
                    <not_has_text text="0.03"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with constaxonomy/otucorr/corraxes file -->
            <param name="accnos" value="amazon.accnos.otulabels"/>
            <param name="intype" value="in_other"/>
            <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
            <output name="pick_out" ftype="mothur.axes">
                <assert_contents>
                    <expand macro="test-axes-format"/>
                    <has_text text="U68686"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The remove.otus command removes otu labels from cons.taxonomy, corr.axes, otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.

.. _remove.otus: https://www.mothur.org/wiki/Remove.otus

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