annotate lordec.xml @ 7:c126b04edfd2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd

<tool id="lordec" name="Lordec" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
    <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
    <macros>
        <token name="@TOOL_VERSION@">0.9</token>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">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>
                        <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" />
                    </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="${tool.name} on ${on_string}: Corrected long reads" >
            <filter>program_type_choice['program_type'] == 'correct'</filter>
        </data>
        <data format="fasta" name="trimmed_reads_file" label="${tool.name} on ${on_string}: Trimmed reads" >
            <filter>program_type_choice['program_type'] == 'trim'</filter>
        </data>
        <data format="tabular" name="stat_file" label="${tool.name} on ${on_string}: Stats" >
            <filter>program_type_choice['program_type'] == 'stats'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <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[

**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>