<tool id="metaspades" name="metaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>metagenome assembler</description>    
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[

#set $library = 1

@PREPROCESS_INPUT_FILES_MAIN@
#if $additional_reads.selector == 'true'
    @PREPROCESS_INPUT_FILES_ADDITIONAL@
#end if
@PREPROCESS_NANOPORE_PACBIO_FILES@

@OMP_THREADS@
## run
metaspades.py
    -o 'output'
    @RESOURCES@
    @INPUT_READS_MAIN@
    #if $additional_reads.selector == 'true'
        @INPUT_READS_ADDITIONAL@
    #end if
    ## reads
    @NANOPORE_PACBIO@
    ## parameter
    @KMER@
    @PHREDOFFSET@
    @PIPELINE_OPTIONS@
    ## postprocessing
    @STATS@
    @CORRECTED@
    ]]></command>
    <inputs>
        <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
        <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/>
        <section name="arf" title="Additional read files">
            <expand macro="nanopore_pacbio"/>
        </section>
        <section name="arf" title="Additional read files">
            <expand macro="nanopore_pacbio"/>
        </section>
        <expand macro="kmer"/>
        <expand macro="phred"/>
        <expand macro="pipeline_options">
            <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
        </expand>
        <expand macro="optional_output"/>
    </inputs>
    <outputs>
        <expand macro="out_ag"/>
        <expand macro="out_ags"/>
        <expand macro="out_cn"/>
        <expand macro="out_cp"/>
        <expand macro="out_cr"/>
        <expand macro="out_cs"/>
        <expand macro="out_l"/>
        <expand macro="out_sc"/>
        <expand macro="out_sp"/>
        <expand macro="out_ss"/>
    </outputs>
    <tests>
        <!-- #1 single, interlaced, fastq.gz, default parameters -->
        <test expect_num_outputs="4">
            <conditional name="singlePaired">
                <param name="sPaired" value="paired_interlaced"/>
                <param name="input1" value="ecoli_1K.fastq.gz"/>
            </conditional>
            <output name="out_ag">
                <assert_contents>
                    <has_n_lines n="36"/>
                    <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106'"/>
                </assert_contents>
            </output>
            <output name="out_ags">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_text_matching expression="S.+"/>
                </assert_contents>
            </output>
            <output name="out_cn">
                <assert_contents>
                    <has_n_lines n="18"/>
                    <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
                </assert_contents>
            </output>
            <output name="out_sc">
                <assert_contents>
                    <has_n_lines n="18"/>
                    <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
                </assert_contents>
            </output>
        </test>
        <!-- #2 single, separate, fastq, default parameters -->
        <test expect_num_outputs="4">
            <conditional name="singlePaired">
                <param name="sPaired" value="paired"/>
                <param name="input1" value="ecoli_1K_1.fastq.gz"/>
                <param name="input2" value="ecoli_1K_2.fastq.gz"/>
            </conditional>
            <output name="out_ag">
                <assert_contents>
                    <has_n_lines n="36"/>
                    <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106'"/>
                </assert_contents>
            </output>
            <output name="out_ags">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_text_matching expression="S.+"/>
                </assert_contents>
            </output>
            <output name="out_cn">
                <assert_contents>
                    <has_n_lines n="18"/>
                    <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
                </assert_contents>
            </output>
            <output name="out_sc">
                <assert_contents>
                    <has_n_lines n="18"/>
                    <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
                </assert_contents>
            </output>
        </test>
        <!-- #3 only corrected reads are created as an output -->
        <test expect_num_outputs="2">
            <conditional name="singlePaired">
                <param name="sPaired" value="paired_interlaced"/>
                <param name="input1" value="ecoli_1K.fastq.gz"/>
            </conditional>
            <param name="optional_output" value="cr,l"/>
            <output_collection name="out_cr" type="list" count="3">
                <element name="ecoli_1K.fastq.gz_1.00.0_0">
                    <assert_contents>
                        <has_size value="130317" delta="5000"/>
                    </assert_contents>
                </element>
                <element name="ecoli_1K.fastq.gz_2.00.0_0">
                    <assert_contents>
                        <has_size value="130317" delta="5000"/>
                    </assert_contents>
                </element>
                <element name="ecoli_1K.fastq.gz__unpaired.00.0_0">
                    <assert_contents>
                        <has_size value="20" delta="5"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="out_l">
                <assert_contents>
                    <has_text_matching expression="Thank you for using SPAdes!"/>
                </assert_contents>
            </output>
        </test>       
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

@HELP_WID@

metaSPAdes is a subtool for assembling metagenomic data sets.

**Input**

@HELP_IN@

**Output**

@HELP_OUT_AG@
@HELP_OUT_AGS@
@HELP_OUT_C@
@HELP_OUT_CP@
@HELP_OUT_CR@
@HELP_OUT_CS@
@HELP_OUT_L@
@HELP_OUT_S@
@HELP_OUT_SP@
@HELP_OUT_SS@

**References**

More information can be found on `github <https://github.com/ablab/spades>`_.
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1101/gr.213959.116</citation>
    </expand>
</tool>