<tool id="qiime_multiple_split_libraries_fastq" name="Run split_libraries_fastq on multiple files" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
    <description>(multiple_split_libraries_fastq)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>multiple_split_libraries_fastq.py -v</version_command>
    <command detect_errors="aggressive"><![CDATA[
mkdir input
&&
#for $i, $s in enumerate( $input_files )
    ln -s '$s.reads' input/reads_${i}.fastq
    &&
    ln -s '$s.barcodes' input/barcodes_${i}.fastq
    &&
    ln -s '$s.mapping' input/mapping_${i}.txt
    &&
#end for
multiple_split_libraries_fastq.py
    --input_dir 'input'
    --output_dir 'output'
    --demultiplexing_method 'mapping_barcode_files'
    #if $parameter_fp
        --parameter_fp '$parameter_fp'
    #end if
    --read_indicator 'reads_'
    --barcode_indicator 'barcodes_'
    --mapping_indicator 'mapping_'
    --mapping_extensions 'txt'
    --leading_text '$leading_text'
    --trailing_text '$trailing_text'
    --sampleid_indicator '.'
    ]]></command>
    <inputs>
        <repeat name="input_files" title="Input files">
            <param name="reads" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Read file"/>
            <param name="barcodes" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Barcode file"/>
            <param name="mapping" type="data" format="txt,tsv,tabular" label="Mapping file"/>
        </repeat>
        <param argument="--demultiplexing_method" type="select" label="Method for demultiplexing">
            <!--<option value="sampleid_by_file" selected="true">Each read file will be used to generate the –sample_ids value passed to split_libraries_fastq.py</option>-->
            <option value="mapping_barcode_file">Search for barcodes and mapping files that match the input read files</option>
        </param>
        <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends"/>
        <param argument="--leading_text" type="text" value="" label="Leading text to add to each join_paired_ends command"/>
        <param argument="--trailing_text" type="text" value="" label="Trailing text to add to each join_paired_ends command"/>
    </inputs>
    <outputs>
        <data name="seq" format="fastq" label="${tool.name} on ${on_string}: Sequences" from_work_dir="output/seqs.fna" />
        <data name="histogram" format="txt" from_work_dir="output/histograms.txt" label="${tool.name} on ${on_string}: Histograms"/>
        <data name="log" format="txt" from_work_dir="output/log_*" label="${tool.name} on ${on_string}: Log"/>
    </outputs>
    <tests>
        <test>
            <repeat name="input_files">
                <param name="reads" value="multiple_split_libraries_fastq/input/reads_1.fastq"/>
                <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_1.fastq"/>
                <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_1.txt"/>
            </repeat>
            <repeat name="input_files">
                <param name="reads" value="multiple_split_libraries_fastq/input/reads_2.fastq"/>
                <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_2.fastq"/>
                <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_2.txt"/>
            </repeat>
            <param name="leading_text" value=""/>
            <param name="trailing_text" value=""/>
            <output name="seq" md5="c146828efa459ec7227fcbcd6e5d4cdc"/>
            <output name="histogram" md5="5f1f73dded81cbed9f1892aabdc2cbb3"/>
        </test>
        <test>
            <repeat name="input_files">
                <param name="reads" value="multiple_split_libraries_fastq/input/reads_1.fastq"/>
                <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_1.fastq"/>
                <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_1.txt"/>
            </repeat>
            <repeat name="input_files">
                <param name="reads" value="multiple_split_libraries_fastq/input/reads_2.fastq"/>
                <param name="barcodes" value="multiple_split_libraries_fastq/input/barcodes_2.fastq"/>
                <param name="mapping" value="multiple_split_libraries_fastq/input/mapping_2.txt"/>
            </repeat>
            <param name="parameter_fp" value="multiple_split_libraries_fastq/qiime_parameters.txt" />
            <param name="leading_text" value=""/>
            <param name="trailing_text" value=""/>
            <output name="seq" md5="c146828efa459ec7227fcbcd6e5d4cdc"/>
            <output name="histogram" md5="5f1f73dded81cbed9f1892aabdc2cbb3"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

In addition to using PCoA, it can be useful to cluster samples using UPGMA (Unweighted Pair Group Method with Arithmetic mean, also known as average linkage). As with PCoA, the input to this step is a distance matrix (i.e. resulting file from beta_diversity.py).
The output is a newick formatted tree compatible with most standard tree viewing programs. Batch processing is also available, allowing the analysis of an entire directory of distance matrices.
    ]]></help>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>