<tool profile="16.07" id="mothur_count_seqs" name="Count.seqs" version="@WRAPPER_VERSION@.0">
    <description>(aka make.table) counts the number of sequences represented by the representative</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 "$name" name.dat &&
        #if $grouping.use == "yes":
            ln -s "$grouping.group" grouping.group.dat &&
        #end if

        echo 'count.seqs(
            name=name.dat,
            #if $grouping.use == "yes":
                group=grouping.group.dat,
                #if $grouping.groups:
                    groups=${ str($grouping.groups).replace(",","-") },
                #end if
            #end if
            large=$large
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
        <conditional name="grouping">
            <param name="use" type="select" label="Use a Group file to include counts for groups">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
                <param name="groups" type="select" label="groups - Groups to display" multiple="true">
                    <help>All groups displayed if none are selected.</help>
                    <options>
                        <filter type="data_meta" ref="group" key="groups"/>
                    </options>
                </param>
            </when>
            <when value="no"/>
        </conditional>
        <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
    </outputs>
    <tests>
        <test><!-- test default params -->
            <param name="name" value="amazon.names"/>
            <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group file -->
            <param name="name" value="amazon.names"/>
            <param name="use" value="yes"/>
            <param name="group" value="amazon.groups"/>
            <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
            <expand macro="logfile-test"/>
        </test>
        <test> <!-- test with group file and subset of groups -->
            <param name="name" value="amazon.names"/>
            <param name="use" value="yes"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="pasture"/>
            <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
            <expand macro="logfile-test"/>
        </test>
        <test> <!-- test with group file and multiple groups -->
            <param name="name" value="amazon.names"/>
            <param name="use" value="yes"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="pasture,forest"/>
            <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown.

.. _name: https://www.mothur.org/wiki/Name_file
.. _group: https://www.mothur.org/wiki/Group_file
.. _count.seqs: https://www.mothur.org/wiki/Count.seqs
.. _count_table: https://www.mothur.org/wiki/Count_File

v.1.21.0: Updated to Mothur 1.33
]]>
    </help>
    <expand macro="citations"/>
</tool>