comparison artic_minion.xml @ 5:7a7d7f30ddfc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"

4:a346730e5552

<tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy2">
    <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[
        mkdir -p 'scheme/name/version' &&
        #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
          ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/version/name.scheme.bed' &&
        #else:
          ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/version/name.scheme.bed' &&
        #end if
        #if str( $reference_source.reference_source_selector ) == "history":
          ln -s '${reference_source.reference}' 'scheme/name/version/name.reference.fasta' &&
          samtools faidx 'scheme/name/version/name.reference.fasta' &&
        #else:
          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"/>

            <when value="history">
                <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence"
                       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" />

            <param name="reference_source_selector" value="history" />
            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
            <param name="reference" value="nCoV-2019.reference.fasta" />
            <param name="primer_scheme_source_selector" value="tool_data_table" />
            <param name="primer_scheme_bedfile" value="test_entry" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
            <param name="reference" value="nCoV-2019.reference.fasta" />
            <param name="primer_scheme_source_selector" value="history" />
            <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.V1.bed" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
        </test>
        <test>
            <param name="reference_source_selector" value="tool_data_table" />
            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
            <param name="reference" value="test_entry" />
            <param name="primer_scheme_source_selector" value="tool_data_table" />
            <param name="primer_scheme_bedfile" value="test_entry" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
        </test>
    </tests>
    <help><![CDATA[
This tool aligns MinION reads that were generated from a tiling amplicon library against a viral reference sequence. 
It generates a consensus fasta file and a vcf variant file.

This tool is configured to use the experimental 'medaka' variant caller.
    ]]></help>
    <citations>
    </citations>
</tool>

5:7a7d7f30ddfc

<tool id="artic_minion" name="ARTIC minion" version="@PACKAGE_VERSION@+galaxy0" profile="20.09">
    <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p 'scheme/name/V1' &&
        #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
          ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/V1/name.scheme.bed' &&
        #else:
          ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/V1/name.scheme.bed' &&
        #end if
        #if str( $reference_source.reference_source_selector ) == "history":
          ln -s '${reference_source.reference}' 'scheme/name/V1/name.reference.fasta' &&
          samtools faidx 'scheme/name/V1/name.reference.fasta' &&
        #else:
          ln -s '${reference_source.reference.fields.path}' 'scheme/name/V1/name.reference.fasta' &&
          samtools faidx 'scheme/name/V1/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
            --medaka-model '$medaka_model'
            $bwa
            'name/V1'
            '${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"/>

            <when value="history">
                <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence"
                       help="You can upload a FASTA sequence to the history and use it as reference" />
            </when>
        </conditional>
        <param type="text" name="medaka_model" label="Medaka model" help="Model string to pass to medaka (see https://github.com/nanoporetech/medaka#models)">
            <validator type="expression" message="Please specify a valid medaka model string (see https://github.com/nanoporetech/medaka#models)">(len(value.strip().split('_')) == 3 or len(value.strip().split('_')) == 4) and value.strip().startswith('r')</validator>
        </param>
    </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" />

            <param name="reference_source_selector" value="history" />
            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
            <param name="reference" value="nCoV-2019.reference.fasta" />
            <param name="primer_scheme_source_selector" value="tool_data_table" />
            <param name="primer_scheme_bedfile" value="test_entry" />
            <param name="medaka_model" value="r941_min_high_g360" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
            <param name="reference" value="nCoV-2019.reference.fasta" />
            <param name="primer_scheme_source_selector" value="history" />
            <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.V1.bed" />
            <param name="medaka_model" value="r941_min_high_g360" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
        </test>
        <test>
            <param name="reference_source_selector" value="tool_data_table" />
            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
            <param name="reference" value="test_entry" />
            <param name="primer_scheme_source_selector" value="tool_data_table" />
            <param name="primer_scheme_bedfile" value="test_entry" />
            <param name="medaka_model" value="r941_min_high_g360" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
        </test>
    </tests>
    <help><![CDATA[
ARTIC_ minion aligns Nanopore reads that were generated from a tiling amplicon library against a viral reference sequence. 
It generates a consensus fasta file and a vcf variant file.

This tool is configured to use the experimental 'medaka' variant caller and must be supplied with the name of
a model file to use with 'medaka', see the `medaka web page`_ for details.

.. _ARTIC: https://artic.readthedocs.io/en/latest/
.. _medaka web page: https://github.com/nanoporetech/medaka#models

Note that you should choose an appropriate model for the medaka version used by ARTIC minion.

==================  ==================
  ARTIC version     medaka version
==================  ==================
 1.2.1                1.0.3
 1.3.0-dev            1.2.3
==================  ==================
    ]]></help>
    <expand macro="citations" />
</tool>