<tool profile="16.07" id="mothur_rename_seqs" name="Rename.seqs" version="@WRAPPER_VERSION@.0">
    <description>Rename sequences by concatenating the group name</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 '$fasta' fasta.dat &&
ln -s '$group' group.dat &&
ln -s '$name' name.dat &&
ln -s '$qfile' qfile.dat &&
ln -s '$contigsreport' contigsreport.dat &&

echo 'rename.seqs(
    fasta=fasta.dat,
    group=group.dat,
    #if $name:
        name=name.dat,
    #end if
    #if $qfile:
        qfile=qfile.dat,
    #end if
    #if $contigsreport:
        contigsreport=contigsreport.dat,
    #end if
    placement=$placement
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="fasta,mothur.align" label="Fasta file"/>
        <param argument="group" type="data" format="mothur.groups" label="Group file"/>
        <param argument="name" type="data" format="mothur.names" optional="true" label="Names file"/>
        <param argument="qfile" type="data" format="qual454" optional="true" label="quality file"/>
        <param argument="contigsreport" type="data" format="tabular" optional="true" label="Contigsreport file"/>
        <param argument="placement" type="select" label="Placement of group name">
            <option value="back" selected="true">back</option>
            <option value="front">front</option>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="group_renamed" format="mothur.groups" from_work_dir="group.renamed.dat" label="${tool.name} on ${on_string}: group_renamed"/>
        <data name="fasta_renamed" format_source="fasta" from_work_dir="fasta.renamed.dat" label="${tool.name} on ${on_string}: fasta_renamed"/>
        <data name="map" format="tabular" from_work_dir="fasta.renamed_map" label="${tool.name} on ${on_string}: renaming map"/>
        <data name="name_renamed" format="mothur.names" from_work_dir="name.renamed.dat" label="${tool.name} on ${on_string}: name_renamed">
            <filter>name</filter>
        </data>
        <data name="qfile_renamed" format="qual454" from_work_dir="qfile.renamed.dat" label="${tool.name} on ${on_string}: qfile_renamed">
            <filter>qfile</filter>
        </data>
        <data name="contigsreport_renamed" format="tabular" from_work_dir="contigsreport.renamed.dat" label="${tool.name} on ${on_string}: contigsreport_renamed">
            <filter>contigsreport</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test with required params -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="group" value="amazon.groups"/>
            <param name="name" value="amazon1.names"/>
            <output name="fasta_renamed" ftype="fasta">
                <assert_contents>
                    <expand macro="test-fasta-format"/>
                    <has_text text="42_forest"/>
                    <has_text text="42_pasture"/>
                </assert_contents>
            </output>
            <output name="map" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_line_matching expression="^42_forest\tU68631$"/>
                </assert_contents>
            </output>
            <output name="group_renamed" ftype="mothur.groups">
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_line_matching expression="^42_forest\tforest$"/>
                </assert_contents>
            </output>
            <output name="name_renamed" ftype="mothur.names">
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_line_matching expression="^42_forest\t42_forest$"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The rename.seqs_ command takes fasta-formatted sequence file and group file, and renames
the sequences by appending the group name to the sequence number.

.. _rename.seqs: https://www.mothur.org/wiki/Rename.seqs

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