comparison lordec.xml @ 6:a32b531f66a0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"

5:6322de5e24e5

<?xml version='1.0' encoding='utf-8'?>
<tool profile="16.04" id="lordec" name="Lordec" version="0.9+galaxy1">
    <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="0.9">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 ${program_type_choice.advanced_options.e}
            #end if
            -T \${GALAXY_SLOTS:-1}
            -o '${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>

                        <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" />
                    </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}" >

        </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" compare="sim_size" delta="10"/>
        </test>
    </tests>
    <help><![CDATA[

6:a32b531f66a0

<tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@">
    <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="0.9">lordec</requirement>
    </requirements>
    <command detect_errors="exit_code"><![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 ${program_type_choice.advanced_options.e}
            #end if
            -T \${GALAXY_SLOTS:-1}
            -o '${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>

                        <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" />
                    </when>
                </conditional>
            </when>
            <when value="trim">
                <param argument="-i" type="data" format="fasta,fasta.gz,fastq,fastq.gz" 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}" >

        </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.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/>
                <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
                <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" ftype="fasta"/>
            </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.gz,lordec/ill-test-5K-2.fa.gz" />
                <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
            </conditional>
            <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/>
        </test>
    </tests>
    <help><![CDATA[