<tool profile="16.07" id="mothur_cluster_fragments" name="Cluster.fragments" version="@WRAPPER_VERSION@.0">
    <description> Group sequences that are part of a larger sequence</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 '$fasta' fasta.dat &&
ln -s '$names' names.dat &&
ln -s '$count' count.dat &&

echo 'cluster.fragments(
    fasta=fasta.dat,
    diffs=$diffs,
    percent=$percent,
    #if $count:
        count=count.dat,
    #end if
    name=names.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
        <param argument="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
        <param argument="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
        <param argument="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
               help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less
               than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like:
               If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.fragclust.fasta" label="${tool.name} on ${on_string}: fasta"/>
        <data name="out_names" format="mothur.names" from_work_dir="fasta*.fragclust.names" label="${tool.name} on ${on_string}: names"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="names" value="amazon1.names" ftype="mothur.names"/>
            <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/>
            <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The cluster.fragments_ command groups sequences that are part of a larger sequence.

.. _cluster.fragments: https://www.mothur.org/wiki/Cluster.fragments

v1.21: Updated to Mothur 1.33. Added count parameter.

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