Mercurial > repos > dfornika > artic_minion
changeset 3:39c2f17a4ad4 draft
Uploaded
author | dfornika |
---|---|
date | Mon, 08 Jun 2020 21:30:39 +0000 |
parents | 08558c991bf8 |
children | f0dd24083241 |
files | artic_minion.xml |
diffstat | 1 files changed, 20 insertions(+), 15 deletions(-) [+] |
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--- a/artic_minion.xml Wed Apr 29 17:02:01 2020 +0000 +++ b/artic_minion.xml Mon Jun 08 21:30:39 2020 +0000 @@ -1,7 +1,7 @@ -<tool id="artic_minion" name="ARTIC minion" version="1.1.0_rc2+galaxy0"> - <description></description> +<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="1.1.0_rc2">artic</requirement> + <requirement type="package" version="1.1.2">artic</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir -p 'scheme/name/version' && @@ -28,7 +28,7 @@ '${read_file.element_identifier}' ]]></command> <inputs> - <param name="read_file" argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> + <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/> <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/> <conditional name="primer_scheme_source"> @@ -68,35 +68,40 @@ </conditional> </inputs> <outputs> - <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="" /> - <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="" /> - <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="" /> - <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="" /> + <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${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_250_1.fastq" /> + <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_250_1.fastq.consensus.fasta" /> + <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_250_1.fastq" /> + <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.V3.bed" /> - <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" /> + <param name="primer_scheme_bedfile" value="nCoV-2019.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_250_1.fastq" /> + <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_250_1.fastq.consensus.fasta" /> + <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" /> </test> </tests> <help><![CDATA[