| Previous changeset 2:376a706dda11 (2020-06-10) Next changeset 4:a346730e5552 (2020-10-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 54e51c32ac2c1fdc5391ee44f749cf6617db5acb" |
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modified:
artic_minion.xml |
| b |
| diff -r 376a706dda11 -r 94020e19b46c artic_minion.xml --- a/artic_minion.xml Wed Jun 10 18:36:36 2020 -0400 +++ b/artic_minion.xml Tue Sep 29 20:20:01 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy0"> +<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> @@ -19,17 +19,22 @@ #end if artic minion --threads \${GALAXY_SLOTS:-1} - --normalise '${normalise}' + #if $normalise > 0: + --normalise ${normalise} + #end if --read-file '${read_file}' --scheme-directory 'scheme' --medaka $bwa 'name/version' '${read_file.element_identifier}' + && bgzip -f '${read_file.element_identifier}.fail.vcf' ]]></command> <inputs> <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> - <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/> + <param argument="--normalise" type="integer" min="0" value="0" + label="Coverage normalisation depth" + help="Sample at most this number of reads per amplicon and strand. default=0 (use all reads)" /> <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/> <conditional name="primer_scheme_source"> <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?" @@ -68,14 +73,13 @@ </conditional> </inputs> <outputs> - <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${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 ${on_string}: variants fail" /> + <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${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 ${on_string}: consensus sequence" /> - <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" /> - <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: coverage mask" /> + <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${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> |