comparison artic_minion.xml @ 4:a346730e5552 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 0c155c65c6499d62ce2ff020c1a904d6b959adb0"

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[

    <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>

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[

    <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 ${on_string}: variants fail" />
        <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${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>