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comparison artic_minion.xml @ 5:7a7d7f30ddfc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
author iuc
date Fri, 27 Aug 2021 20:34:32 +0000
parents a346730e5552
children f212134e204c
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4:a346730e5552 5:7a7d7f30ddfc
1 <tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy2"> 1 <tool id="artic_minion" name="ARTIC minion" version="@PACKAGE_VERSION@+galaxy0" profile="20.09">
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 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.1.3">artic</requirement> 7 <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 mkdir -p 'scheme/name/version' && 10 mkdir -p 'scheme/name/V1' &&
8 #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table": 11 #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
9 ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/version/name.scheme.bed' && 12 ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/V1/name.scheme.bed' &&
10 #else: 13 #else:
11 ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/version/name.scheme.bed' && 14 ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/V1/name.scheme.bed' &&
12 #end if 15 #end if
13 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
14 ln -s '${reference_source.reference}' 'scheme/name/version/name.reference.fasta' && 17 ln -s '${reference_source.reference}' 'scheme/name/V1/name.reference.fasta' &&
15 samtools faidx 'scheme/name/version/name.reference.fasta' && 18 samtools faidx 'scheme/name/V1/name.reference.fasta' &&
16 #else: 19 #else:
17 ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' && 20 ln -s '${reference_source.reference.fields.path}' 'scheme/name/V1/name.reference.fasta' &&
18 samtools faidx 'scheme/name/version/name.reference.fasta' && 21 samtools faidx 'scheme/name/V1/name.reference.fasta' &&
19 #end if 22 #end if
20 artic minion 23 artic minion
21 --threads \${GALAXY_SLOTS:-1} 24 --threads \${GALAXY_SLOTS:-1}
22 #if $normalise > 0: 25 #if $normalise > 0:
23 --normalise ${normalise} 26 --normalise ${normalise}
24 #end if 27 #end if
25 --read-file '${read_file}' 28 --read-file '${read_file}'
26 --scheme-directory 'scheme' 29 --scheme-directory 'scheme'
27 --medaka 30 --medaka
31 --medaka-model '$medaka_model'
28 $bwa 32 $bwa
29 'name/version' 33 'name/V1'
30 '${read_file.element_identifier}' 34 '${read_file.element_identifier}'
31 && bgzip -f '${read_file.element_identifier}.fail.vcf' 35 && bgzip -f '${read_file.element_identifier}.fail.vcf'
32 ]]></command> 36 ]]></command>
33 <inputs> 37 <inputs>
34 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/> 38 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
69 <when value="history"> 73 <when value="history">
70 <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence" 74 <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence"
71 help="You can upload a FASTA sequence to the history and use it as reference" /> 75 help="You can upload a FASTA sequence to the history and use it as reference" />
72 </when> 76 </when>
73 </conditional> 77 </conditional>
78 <param type="text" name="medaka_model" label="Medaka model" help="Model string to pass to medaka (see https://github.com/nanoporetech/medaka#models)">
79 <validator type="expression" message="Please specify a valid medaka model string (see https://github.com/nanoporetech/medaka#models)">(len(value.strip().split('_')) == 3 or len(value.strip().split('_')) == 4) and value.strip().startswith('r')</validator>
80 </param>
74 </inputs> 81 </inputs>
75 <outputs> 82 <outputs>
76 <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${tool.name} on ${on_string}: trimmed alignment" /> 83 <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
77 <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" /> 84 <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
78 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: medaka variant calls" /> 85 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: medaka variant calls" />
87 <param name="reference_source_selector" value="history" /> 94 <param name="reference_source_selector" value="history" />
88 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" /> 95 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
89 <param name="reference" value="nCoV-2019.reference.fasta" /> 96 <param name="reference" value="nCoV-2019.reference.fasta" />
90 <param name="primer_scheme_source_selector" value="tool_data_table" /> 97 <param name="primer_scheme_source_selector" value="tool_data_table" />
91 <param name="primer_scheme_bedfile" value="test_entry" /> 98 <param name="primer_scheme_bedfile" value="test_entry" />
99 <param name="medaka_model" value="r941_min_high_g360" />
92 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" /> 100 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
93 </test> 101 </test>
94 <test> 102 <test>
95 <param name="reference_source_selector" value="history" /> 103 <param name="reference_source_selector" value="history" />
96 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" /> 104 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
97 <param name="reference" value="nCoV-2019.reference.fasta" /> 105 <param name="reference" value="nCoV-2019.reference.fasta" />
98 <param name="primer_scheme_source_selector" value="history" /> 106 <param name="primer_scheme_source_selector" value="history" />
99 <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.V1.bed" /> 107 <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.V1.bed" />
108 <param name="medaka_model" value="r941_min_high_g360" />
100 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" /> 109 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
101 </test> 110 </test>
102 <test> 111 <test>
103 <param name="reference_source_selector" value="tool_data_table" /> 112 <param name="reference_source_selector" value="tool_data_table" />
104 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" /> 113 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
105 <param name="reference" value="test_entry" /> 114 <param name="reference" value="test_entry" />
106 <param name="primer_scheme_source_selector" value="tool_data_table" /> 115 <param name="primer_scheme_source_selector" value="tool_data_table" />
107 <param name="primer_scheme_bedfile" value="test_entry" /> 116 <param name="primer_scheme_bedfile" value="test_entry" />
117 <param name="medaka_model" value="r941_min_high_g360" />
108 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" /> 118 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
109 </test> 119 </test>
110 </tests> 120 </tests>
111 <help><![CDATA[ 121 <help><![CDATA[
112 This tool aligns MinION reads that were generated from a tiling amplicon library against a viral reference sequence. 122 ARTIC_ minion aligns Nanopore reads that were generated from a tiling amplicon library against a viral reference sequence.
113 It generates a consensus fasta file and a vcf variant file. 123 It generates a consensus fasta file and a vcf variant file.
114 124
115 This tool is configured to use the experimental 'medaka' variant caller. 125 This tool is configured to use the experimental 'medaka' variant caller and must be supplied with the name of
126 a model file to use with 'medaka', see the `medaka web page`_ for details.
127
128 .. _ARTIC: https://artic.readthedocs.io/en/latest/
129 .. _medaka web page: https://github.com/nanoporetech/medaka#models
130
131 Note that you should choose an appropriate model for the medaka version used by ARTIC minion.
132
133 ================== ==================
134 ARTIC version medaka version
135 ================== ==================
136 1.2.1 1.0.3
137 1.3.0-dev 1.2.3
138 ================== ==================
116 ]]></help> 139 ]]></help>
117 <citations> 140 <expand macro="citations" />
118 </citations>
119 </tool> 141 </tool>