comparison artic_minion.xml @ 3:94020e19b46c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 54e51c32ac2c1fdc5391ee44f749cf6617db5acb"

2:376a706dda11

<tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy0">
    <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
    <requirements>
        <requirement type="package" version="1.1.3">artic</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

          ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' &&
          samtools faidx 'scheme/name/version/name.reference.fasta' &&
        #end if
        artic minion
            --threads \${GALAXY_SLOTS:-1}
            --normalise '${normalise}'
            --read-file '${read_file}'
            --scheme-directory 'scheme'
            --medaka
            $bwa
            'name/version'
            '${read_file.element_identifier}'
    ]]></command>
    <inputs>
        <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
        <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/>
        <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
        <conditional name="primer_scheme_source">
            <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?"
                   help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
                <option value="tool_data_table">From tool data table</option>

                       help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
        <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" />
        <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants merged" />
        <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${tool.name} on ${on_string}: variants pass" />
        <data name="variants_fail_vcf" format="vcf" from_work_dir="*.fail.vcf" label="${tool.name} on ${on_string}: variants fail" />
        <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
        <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
        <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: coverage mask" />
        <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history" />

3:94020e19b46c

<tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy1">
    <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
    <requirements>
        <requirement type="package" version="1.1.3">artic</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

          ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' &&
          samtools faidx 'scheme/name/version/name.reference.fasta' &&
        #end if
        artic minion
            --threads \${GALAXY_SLOTS:-1}
        #if $normalise > 0:
            --normalise ${normalise}
        #end if
            --read-file '${read_file}'
            --scheme-directory 'scheme'
            --medaka
            $bwa
            'name/version'
            '${read_file.element_identifier}'
        && bgzip -f '${read_file.element_identifier}.fail.vcf'
    ]]></command>
    <inputs>
        <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
        <param argument="--normalise" type="integer" min="0" value="0"
        label="Coverage normalisation depth"
        help="Sample at most this number of reads per amplicon and strand. default=0 (use all reads)" />
        <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
        <conditional name="primer_scheme_source">
            <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?"
                   help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
                <option value="tool_data_table">From tool data table</option>

                       help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
        <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
        <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: medaka variant calls" />
        <data name="variants_fail_vcf" format="vcf_bgzip" from_work_dir="*.fail.vcf.gz" label="${tool.name} on ${on_string}: variants fail" />
        <data name="variants_pass_vcf" format="vcf" from_work_dir="*.pass.vcf" label="${tool.name} on ${on_string}: variants pass" />
        <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
        <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: consensus coverage mask" />
        <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history" />