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comparison artic_minion.xml @ 3:94020e19b46c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 54e51c32ac2c1fdc5391ee44f749cf6617db5acb"
author iuc
date Tue, 29 Sep 2020 20:20:01 +0000
parents 376a706dda11
children a346730e5552
comparison
equal deleted inserted replaced
2:376a706dda11 3:94020e19b46c
1 <tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy0"> 1 <tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy1">
2 <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description> 2 <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.3">artic</requirement> 4 <requirement type="package" version="1.1.3">artic</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
17 ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' && 17 ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' &&
18 samtools faidx 'scheme/name/version/name.reference.fasta' && 18 samtools faidx 'scheme/name/version/name.reference.fasta' &&
19 #end if 19 #end if
20 artic minion 20 artic minion
21 --threads \${GALAXY_SLOTS:-1} 21 --threads \${GALAXY_SLOTS:-1}
22 --normalise '${normalise}' 22 #if $normalise > 0:
23 --normalise ${normalise}
24 #end if
23 --read-file '${read_file}' 25 --read-file '${read_file}'
24 --scheme-directory 'scheme' 26 --scheme-directory 'scheme'
25 --medaka 27 --medaka
26 $bwa 28 $bwa
27 'name/version' 29 'name/version'
28 '${read_file.element_identifier}' 30 '${read_file.element_identifier}'
31 && bgzip -f '${read_file.element_identifier}.fail.vcf'
29 ]]></command> 32 ]]></command>
30 <inputs> 33 <inputs>
31 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> 34 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
32 <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/> 35 <param argument="--normalise" type="integer" min="0" value="0"
36 label="Coverage normalisation depth"
37 help="Sample at most this number of reads per amplicon and strand. default=0 (use all reads)" />
33 <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/> 38 <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
34 <conditional name="primer_scheme_source"> 39 <conditional name="primer_scheme_source">
35 <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?" 40 <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?"
36 help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table"> 41 help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
37 <option value="tool_data_table">From tool data table</option> 42 <option value="tool_data_table">From tool data table</option>
66 help="You can upload a FASTA sequence to the history and use it as reference" /> 71 help="You can upload a FASTA sequence to the history and use it as reference" />
67 </when> 72 </when>
68 </conditional> 73 </conditional>
69 </inputs> 74 </inputs>
70 <outputs> 75 <outputs>
71 <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" /> 76 <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
72 <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" /> 77 <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
73 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants merged" /> 78 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: medaka variant calls" />
74 <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${tool.name} on ${on_string}: variants pass" /> 79 <data name="variants_fail_vcf" format="vcf_bgzip" from_work_dir="*.fail.vcf.gz" label="${tool.name} on ${on_string}: variants fail" />
75 <data name="variants_fail_vcf" format="vcf" from_work_dir="*.fail.vcf" label="${tool.name} on ${on_string}: variants fail" /> 80 <data name="variants_pass_vcf" format="vcf" from_work_dir="*.pass.vcf" label="${tool.name} on ${on_string}: variants pass" />
76 <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" /> 81 <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
77 <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" /> 82 <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: consensus coverage mask" />
78 <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: coverage mask" />
79 <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" /> 83 <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
80 </outputs> 84 </outputs>
81 <tests> 85 <tests>
82 <test> 86 <test>
83 <param name="reference_source_selector" value="history" /> 87 <param name="reference_source_selector" value="history" />