<tool profile="16.07" id="mothur_merge_files" name="Merge.files" version="@WRAPPER_VERSION@.0">
    <description>Merge data</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
#for $i in $merge.inputs:
    ln -s '$i' input${merge.inputs.index($i)}.dat &&
#end for

echo 'merge.files(
    input=#for $i in $merge.inputs#input${merge.inputs.index($i)}.dat-#end for#,
    output=$output
)'
| sed 's/ //g'  ## mothur trips over whitespace
| sed 's/-,/,/g'
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
    <conditional name="merge">
        <param name="type" type="select" format="fasta,qual,mothur.groups,mothur.names,mothur.accnos" label="Merge">
            <option value="fasta">fasta files</option>
            <option value="qual">qual files</option>
            <option value="groups">group files</option>
            <option value="names">name files</option>
            <option value="accnos">accnos files</option>
        </param>
        <when value="fasta">
            <param name="inputs" type="data" format="fasta" multiple="true" label="inputs - fasta"/>
        </when> <!-- fasta -->
        <when value="qual">
            <param name="inputs" type="data" format="qual" multiple="true" label="inputs - qual"/>
        </when> <!-- qual -->
        <when value="groups">
            <param name="inputs" type="data" format="mothur.groups" multiple="true" label="inputs - groups"/>
        </when> <!-- groups -->
        <when value="names">
            <param name="inputs" type="data" format="mothur.names" multiple="true" label="inputs - names"/>
        </when> <!-- names -->
        <when value="accnos">
            <param name="inputs" type="data" format="mothur.accnos" multiple="true" label="inputs - accnos"/>
        </when> <!-- fasta -->
    </conditional> <!-- merge -->
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data format_source="inputs" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
    </outputs>
    <tests>
        <test>
            <param name="type" value="fasta"/>
            <param name="inputs" value="sample1.fa,sample2.fa,sample3.fa" ftype="fasta"/>
            <output name="output" file="output.fa" ftype="fasta"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[
@MOTHUR_OVERVIEW@

**Command Documentation**

The merge.files_ command merge inputs into a single output.

.. _merge.files: https://www.mothur.org/wiki/Merge.files


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