<macros>
    <!-- not yet finished -->
    <token name="@SALMON_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_2@
            #if str($repeat2.type.type) == "meta"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
                    #set file_path = os.path.join($file_dir, 'meta_info.json')
                    mkdir '$file_dir' &&
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type.type) == "fld"
                #for $k, $file in enumerate($repeat2.type.input)
                    #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
                    #set file_path = os.path.join($file_dir,'flenDist.txt')
                    mkdir '$file_dir' &&
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    ]]></token>
    <xml name="salmon_form">

    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="salmon_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="trimmomatic"/>
                    <param name="input" value="trimmomatic.txt"/>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report"/>
                    <has_text text="Commment for the report"/>
                    <has_text text="cutadapt_trimmed_sequences_plot"/>
                    <has_text text="All-in-one FASTQ preprocessor"/>
                    <has_text text="trimmomatic_plot"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="dataset_33"/>
                    <has_text text="R1_fq"/>
                    <has_text text="result_right"/>
                    <has_text text="25839_merged"/>
                    <has_text text="C2"/>
                    <has_n_lines n="11"/>
                    <has_n_columns n="22"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="29"/>
        </test>
    </xml>
</macros>