comparison artic_minion.xml @ 1:20165d3a8fb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 125ea4d98050db32bae4f722ef153305e8d48a94"

0:c411e2205442

<tool id="artic_minion" name="ARTIC minion" version="1.1.0_rc2+galaxy0">
    <description></description>
    <requirements>
        <requirement type="package" version="1.1.0_rc2">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' &&

                   help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
                <option value="tool_data_table">From tool data table</option>
                <option value="history">From history</option>
            </param>
            <when value="tool_data_table">
                <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme">
	            <options from_data_table="primer_scheme_bedfiles">
	                <validator type="no_options" message="No primer scheme .bed files are available" />
                    </options>
	        </param>
            </when>
            <when value="history">
                <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" />
            </when>
        </conditional>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in reference?" >
                <option value="cached">Use a built-in reference</option>

        </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 ${on_string}: variants vcf" />
        <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
    </outputs>
    <tests>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="read_file" value="SRR11410539_seqtk_sample_250_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_250_1.fastq.consensus.fasta" />
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="read_file" value="SRR11410539_seqtk_sample_250_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.V1.bed" />
            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
        </test>
        <test>
            <param name="reference_source_selector" value="tool_data_table" />
            <param name="read_file" value="SRR11410539_seqtk_sample_250_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_250_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.

1:20165d3a8fb1

<tool id="artic_minion" name="ARTIC minion" version="1.1.2+galaxy0">
    <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
    <requirements>
        <requirement type="package" version="1.1.2">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' &&

                   help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
                <option value="tool_data_table">From tool data table</option>
                <option value="history">From history</option>
            </param>
            <when value="tool_data_table">
                <param name="primer_scheme_bedfile" type="select" format="tabular" label="Primer Scheme">
	            <options from_data_table="primer_scheme_bedfiles">
	                <validator type="no_options" message="No primer scheme .bed files are available" />
                    </options>
	        </param>
            </when>
            <when value="history">
                <param name="primer_scheme_bedfile" type="data" format="tabular" label="Primer Scheme" />
            </when>
        </conditional>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in reference?" >
                <option value="cached">Use a built-in reference</option>

        </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" />
            <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.