<tool id="badread" name="Badread" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" python_template_version="3.5" profile="21.05">

    <description>long-read simulator</description>
    <macros>
        <token name="@TOOL_VERSION@">0.4.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_2426</edam_operation> <!-- Modelling and simulation -->
    </edam_operations>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">badread</requirement>
        <requirement type="package" version="2.8">pigz</requirement>
    </requirements>
    <version_command>badread --version | perl -wpe 's/Badread v//'</version_command>

    <command detect_errors="aggressive"><![CDATA[
        badread simulate 
          --reference '${io.reference}'
          --quantity '${sim.quantity}'
          --length '${sim.length}'
          --identity '${sim.identity}'
          --error_model '${sim.error_model}'
          --qscore_model '${sim.qscore_model}'
          #if str($sim.seed.seed_bool) == "True":
            --seed ${sim.seed.seed}
          #end if
          --start_adapter '${adapt.start_adapter}'
          --end_adapter '${adapt.end_adapter}'
          --start_adapter_seq '${adapt.start_adapter_seq}'
          --end_adapter_seq '${adapt.end_adapter_seq}'
          --junk_reads ${problems.junk_reads}
          --random_reads ${problems.random_reads}
          --chimera ${problems.chimera}
          --glitches '${problems.glitches}'
          $small_plasmid_bias
          ${io.compress_output}
        > $output
    ]]></command>

    <inputs>
        <section name="io" title="Input/Output" expanded="true">
            <param type="data"
                argument="--reference"
                format="fasta,fasta.gz"
                label="Reference"
                help="Reference file in FASTA format"/>
            <param type="boolean"
                name="compress_output"
                checked="true"
                truevalue="| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time"
                falsevalue=""
                label="Compress output" />
        </section>
        <section name="sim" title="Simulation parameters" expanded="true">
            <param type="text"
                optional="false"
                argument="--quantity"
                label="Quantity"
                help="Absolute number of bp (e.g. '250M') or relative depth (e.g. '25x')">
                <validator type="regex">^\d+(?i:[xkmg])?$</validator>
                <validator type="empty_field" />
            </param>
            <param type="text"
                argument="--length"
                value="15000,13000"
                label="Fragment length distribution"
                help="'mean,stdev'">
                <validator type="regex">^\d+,\d+$</validator>
            </param>
            <param type="text"
                argument="--identity"
                value="95,99,2.5"
                label="Identity distribution"
                help="'mean,max,stdev' for identity beta distribution, 'mean,stdev' for qscore normal distribution">
                <validator type="regex">^[\d\.]+,[\d\.]+(,[\d\.]+)?$</validator>
            </param>
            <param type="select" argument="--error_model" label="Error model">
                <option value="nanopore2018">nanopore2018</option>
                <option value="nanopore2020">nanopore2020</option>
                <option value="nanopore2023" selected="true">nanopore2023</option>
                <option value="pacbio2016">pacbio2016</option>
                <option value="pacbio2021">pacbio2021</option>
                <option value="random">random</option>
            </param>
            <param type="select" argument="--qscore_model" label="Q-score model">
                <option value="nanopore2018">nanopore2018</option>
                <option value="nanopore2020">nanopore2020</option>
                <option value="nanopore2023" selected="true">nanopore2023</option>
                <option value="pacbio2016">pacbio2016</option>
                <option value="pacbio2021">pacbio2021</option>
                <option value="random">random</option>
                <option value="ideal">ideal</option>
            </param>
            <conditional name="seed">
                <param name="seed_bool" type="select" label="Fixed seed?">
                    <option value="False" selected="true">No</option>
                    <option value="True">Yes</option>
                </param>
                <when value="True">
                    <param argument="--seed" type="integer" value="1234" label="Enter seed" />
                </when>
                <when value="False" />
            </conditional>
        </section>
        <section name="adapt" title="Adapters">
            <param type="text"
                argument="--start_adapter"
                value="90,60"
                label="Start adapter"
                help="'rate,amount'">
                <validator type="regex">^\d+,\d+$</validator>
            </param>
            <param type="text"
                argument="--end_adapter"
                value="50,20"
                label="End adapter"
                help="'rate,amount'">
                <validator type="regex">^\d+,\d+$</validator>
            </param>
            <param type="text"
                argument="--start_adapter_seq"
                value="AATGTACTTCGTTCAGTTACGTATTGCT"
                label="Start adapter sequence">
                <validator type="regex">^(?i:[ATGC]+)$</validator>
            </param>
            <param type="text"
                argument="--end_adapter_seq"
                value="GCAATACGTAACTGAACGAAGT"
                label="End adapter sequence">
                <validator type="regex">^(?i:[ATGC]+)$</validator>
            </param>
        </section>
        <section name="problems" title="Problems">
            <param type="float"
                argument="--junk_reads"
                value="1"
                min="0"
                max="100"
                label="Percentage junk reads"
                help="0-100" />
            <param type="float"
                argument="--random_reads"
                value="1"
                min="0"
                max="100"
                label="Percentage random reads"
                help="0-100" />
            <param type="float"
                argument="--chimera"
                value="1"
                min="0"
                max="50"
                label="Percentage chimeric formation"
                help="0-50" />
            <param type="text"
                argument="--glitches"
                value="10000,25,25"
                label="Read glitches"
                help="'rate,size,skip'">
                <validator type="regex">^\d+,\d+,\d+$</validator>
            </param>
            <param type="boolean"
                argument="--small_plasmid_bias"
                checked="false"
                truevalue="--small_plasmid_bias"
                falsevalue=""
                label="Small plasmid bias"
                help="Drop circular sequences smaller than fragment length" />
        </section>
    </inputs>

    <outputs>
        <data name="output" format="fastq.gz">
            <change_format>
                <when input="io.compress_output" value="" format="fastq" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <!-- defaults with seed -->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <output name="output" file="2x.fq.gz" compare="diff" ftype="fastq.gz" decompress="true" />
            <assert_command>
                <has_text text="--seed 22" />
            </assert_command>
        </test>
        <!-- defaults without seed -->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="quantity" value="2x" />
            <assert_command>
                <not_has_text text="--seed " />
            </assert_command>
        </test>
        <!-- use absolute quanitity w/o compression-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="50k" />
            <param name="compress_output" value="false" />
            <output name="output" file="50k.fq.gz" compare="diff" ftype="fastq" decompress="true" />
        </test>
        <!-- set length dist-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <param name="length" value="2000,1000" />
            <output name="output" file="2x.l2000_1000.fq.gz" compare="diff" decompress="true" />
        </test>
        <!-- set identity as beta dist-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <param name="identity" value="80,90,5" />
            <output name="output" file="2x.i80_90_5.fq.gz" compare="diff" decompress="true" />
            <assert_stderr>
                <has_text text="identities from a beta distribution" />
            </assert_stderr>
        </test>
        <!-- set identity as normal dist-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <param name="identity" value="80,5" />
            <output name="output" file="2x.i80_5.fq.gz" compare="diff" decompress="true" />
            <assert_stderr>
                <has_text text="qscores from a normal distribution" />
            </assert_stderr>
        </test>
        <!-- other models -->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <param name="error_model" value="pacbio2021" />
            <param name="qscore_model" value="pacbio2021" />
            <output name="output" file="2x.em_pacbio2021.qm_pacbio2021.fq.gz" compare="diff" decompress="true" />
        </test>
        <!-- set non-default adapters-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <param name="start_adapter" value="50,30" />
            <param name="start_adapter_seq" value="ATGC" />
            <param name="end_adapter" value="80,40" />
            <param name="end_adapter_seq" value="GCAT" />
            <output name="output" file="2x.sa50_30_ATGC.ea80_40_GCAT.fq.gz" compare="diff" decompress="true" />
        </test>
        <!-- set problem parameters-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="2x" />
            <param name="junk_reads" value="80" />
            <param name="random_reads" value="9.5" />
            <param name="chimera" value="5" />
            <param name="glitches" value="2000,50,40" />
            <output name="output" file="2x.j80.r9.5.c5.g2000_50_40.fq.gz" compare="diff" decompress="true" />
        </test>
        <!-- without and with small plasmid bias-->
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="1M" />
            <output name="output" decompress="true">
                <assert_contents>
                    <has_text text="GU320569" />
                </assert_contents>
            </output>   
        </test>
        <test>
            <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
            <param name="seed_bool" value="True" />
            <param name="seed" value="22" />
            <param name="quantity" value="1M" />
            <param name="small_plasmid_bias" value="true" />
            <output name="output" decompress="true">
                <assert_contents>
                    <not_has_text text="GU320569" />
                </assert_contents>
            </output>   
        </test>
    </tests>

    <help><![CDATA[
**Required arguments:**

  --reference REFERENCE         Reference FASTA file (can be gzipped)
  --quantity QUANTITY           Either an absolute value (e.g. 250M) or a
                                relative depth (e.g. 25x)

**Simulation parameters:**

  --length LENGTH               Fragment length distribution (mean and stdev,
                                default: 15000,13000)
  --identity IDENTITY           Sequencing identity distribution
                                (mean,max,stdev for beta distribution or
                                mean,stdev for normal qscore distribution,
                                default: 95,99,2.5)
  --error_model ERROR_MODEL     Can be "nanopore2018", "nanopore2020",
                                "nanopore2023", "pacbio2016", "pacbio2021",
                                "random" or a model filename (default:
                                nanopore2023)
  --qscore_model QSCORE_MODEL   Can be "nanopore2018", "nanopore2020",
                                "nanopore2023", "pacbio2016", "pacbio2021",
                                "random", "ideal" or a model filename
                                (default: nanopore2023)
  --seed SEED                   Random number generator seed for deterministic
                                output (default: different output each time)

**Adapters:**

  --start_adapter START_ADAPTER
                                Adapter parameters for read starts (rate and
                                amount, default: 90,60)
  --end_adapter END_ADAPTER     Adapter parameters for read ends (rate and
                                amount, default: 50,20)
  --start_adapter_seq START_ADAPTER_SEQ
                                Adapter sequence for read starts (default:
                                AATGTACTTCGTTCAGTTACGTATTGCT)
  --end_adapter_seq END_ADAPTER_SEQ
                                Adapter sequence for read ends (default:
                                GCAATACGTAACTGAACGAAGT)

**Problems:**

  --junk_reads JUNK_READS       This percentage of reads will be
                                low-complexity junk (default: 1)
  --random_reads RANDOM_READS   This percentage of reads will be random
                                sequence (default: 1)
  --chimeras CHIMERAS           Percentage at which separate fragments join
                                together (default: 1)
  --glitches GLITCHES           Read glitch parameters (rate, size and skip,
                                default: 10000,25,25)
  --small_plasmid_bias          If set, then small circular plasmids are lost
                                when the fragment length is too high (default:
                                small plasmids are included regardless of
                                fragment length)

    ]]></help>

    <citations>
        <citation type="doi">10.21105/joss.01316</citation>
    </citations>

</tool>