<?xml version='1.0' encoding='utf-8'?>
<tool profile="16.04" id="lordec" name="Lordec" version="0.6">
    <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.6">lordec</requirement>
    </requirements>
    <command><![CDATA[

        #if str( $program_type_choice.program_type ) == "correct"
            lordec-correct
            @lordec_inputs@
            #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced"
                -t ${program_type_choice.advanced_options.t}
                -b ${program_type_choice.advanced_options.b}
                -e ${program_type_choice.advanced_options.e}
                -T ${program_type_choice.advanced_options.T}
            #end if
            -o '${corrected_read_file}'


        #else if str( $program_type_choice.program_type ) == "trim"
            #if $program_type_choice.split
                lordec-trim-split
            #else
                lordec-trim
            #end if
            -i '${program_type_choice.i}'
            -o '${trimmed_reads_file}'

        #else
            lordec-stat
            @lordec_inputs@
            -S '${stat_file}'
        #end if


    ]]></command>

    <inputs>

        <conditional name="program_type_choice">
            <param name="program_type" type="select" label="Choose Lordec program">
                <option value="correct">Lordec Correct</option>
                <option value="trim">Lordec Trim</option>
                <option value="stats">Lordec Statistics</option>
            </param>

            <when value="correct">
                <expand macro="lordec_inputs" />
                <conditional name="advanced_options">
                    <param name="advanced_options_selector" type="select" label="Lordec correct advanced options">
                        <option value="default" selected="true">Default</option>
                        <option value="advanced">Advanced</option>
                    </param>
                    <when value="default"></when>
                    <when value="advanced">
                        <param argument="-t" type="integer" label="Number of target k-mers" value="5" />
                        <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" />
                        <param argument="-e" type="float" label="Maximum error rate" value="0.4" />
                        <param argument="-T" type="integer" label="Number of threads" value="1" />
                    </when>
                </conditional>
            </when>

            <when value="trim">
                <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
                <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" />
            </when>

            <when value="stats">
                <expand macro="lordec_inputs" />
            </when>

        </conditional>

    </inputs>

    <outputs>
        <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
            <filter>program_type_choice['program_type'] == 'correct'</filter>
        </data>
        <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
            <filter>program_type_choice['program_type'] == 'trim'</filter>
        </data>
        <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
            <filter>program_type_choice['program_type'] == 'stats'</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <conditional name="program_type_choice">
                <param name="program_type" value="correct" />
                <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
                <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
                <param name="k" value="31" />
            </conditional>
            <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
        </test>
        <test>
            <conditional name="program_type_choice">
                <param name="program_type" value="trim" />
                <param name="i" value="lordec/corrected_reads.fa" />
            </conditional>
            <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
        </test>
        <test>
            <conditional name="program_type_choice">
                <param name="program_type" value="stats" />
                <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
                <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
            </conditional>
            <output name="stat_file" file="lordec/stat_file.txt"/>
        </test>
    </tests>
    <help><![CDATA[

**Lordec Correct**

Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina).

LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters.

-------

**Lordec Trim**

Program for trimming the weak regions from the beginning and end of the corrected reads.

-------

**Lordec Statistics**

Program to generate statistics on solid and weak k-mers.

-------

**Web site**

http://www.atgc-montpellier.fr/lordec/


    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/bioinformatics/btu538</citation>
    </expand>
</tool>