<tool id="ctat_concatenate" name="ctat_concatenate" version="1.0.0" profile="17.05">
    <description> concatenate datasets from tail to head</description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>

    <command detect_errors="exit_code">
      <![CDATA[
        python $__tool_directory__/ctat_bash_command_executer.py cat
        $input1
        #for $q in $queries
            ${q.input2}
        #end for
        > $out_file1 
      ]]>
    </command>
    <inputs>
        <param name="input1" type="data" label="Concatenate Dataset"/>
        <repeat name="queries" title="Dataset">
            <param name="input2" type="data" label="Select" />
        </repeat>
    </inputs>
    <outputs>
        <data name="out_file1" format="input" metadata_source="input1"/>
    </outputs>

    <tests>
        <test>
            <param name="input1" value="Sp_ds.left.fq"/>
            <param name="input2" value="Sp_hs.left.fq"/>
            <output name="out_file1" file="Sp.cat_ds_hs.left.fq">
                <assert_contents>
                    <has_line_matching expression=".+" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input1" value="Sp_ds.right.fq"/>
            <param name="input2" value="Sp_hs.right.fq"/>
            <output name="out_file1" file="Sp.cat_ds_hs.right.fq">
                <assert_contents>
                    <has_line_matching expression=".+" />
                </assert_contents>
            </output>
        </test>
        <!--TODO: if possible, enhance the underlying test code to handle this test
            the problem is multiple params with the same name "input2"
        <test>
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <param name="input2" value="3.bed"/>
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
        </test>
        -->
    </tests>
    <help>
.. class:: infomark 

Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly.

If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.

.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
.. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
    </help>
</tool>