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author dfornika
date Mon, 08 Jun 2020 21:45:15 +0000
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1 <tool id="artic_minion" name="ARTIC minion" version="1.1.2+galaxy0">
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2 <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2">artic</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 mkdir -p 'scheme/name/version' &&
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8 #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
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9 ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/version/name.scheme.bed' &&
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10 #else:
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11 ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/version/name.scheme.bed' &&
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12 #end if
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13 #if str( $reference_source.reference_source_selector ) == "history":
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14 ln -s '${reference_source.reference}' 'scheme/name/version/name.reference.fasta' &&
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15 samtools faidx 'scheme/name/version/name.reference.fasta' &&
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16 #else:
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17 ln -s '${reference_source.reference.fields.path}' 'scheme/name/version/name.reference.fasta' &&
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18 samtools faidx 'scheme/name/version/name.reference.fasta' &&
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19 #end if
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20 artic minion
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21 --threads \${GALAXY_SLOTS:-1}
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22 --normalise '${normalise}'
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23 --read-file '${read_file}'
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24 --scheme-directory 'scheme'
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25 --medaka
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26 $bwa
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27 'name/version'
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28 '${read_file.element_identifier}'
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29 ]]></command>
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30 <inputs>
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31 <param name="read_file" argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
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32 <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/>
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33 <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
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34 <conditional name="primer_scheme_source">
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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?"
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36 help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
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37 <option value="tool_data_table">From tool data table</option>
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38 <option value="history">From history</option>
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39 </param>
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40 <when value="tool_data_table">
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41 <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme">
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42 <options from_data_table="primer_scheme_bedfiles">
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43 <validator type="no_options" message="No primer scheme .bed files are available" />
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44 </options>
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45 </param>
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46 </when>
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47 <when value="history">
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48 <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" />
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49 </when>
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50 </conditional>
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51 <conditional name="reference_source">
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52 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in reference?" >
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53 <option value="cached">Use a built-in reference</option>
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54 <option value="history">Use a reference from history</option>
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55 </param>
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56 <when value="cached">
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57 <param name="reference" type="select" label="Using reference genome" help="Select genome from the list">
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58 <options from_data_table="all_fasta">
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59 <filter type="sort_by" column="2" />
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60 <validator type="no_options" message="No references are available" />
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61 </options>
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62 </param>
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63 </when>
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64 <when value="history">
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65 <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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66 help="You can upload a FASTA sequence to the history and use it as reference" />
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
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72 <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" />
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73 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants merged" />
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74 <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${tool.name} on ${on_string}: variants pass" />
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75 <data name="variants_fail_vcf" format="vcf" from_work_dir="*.fail.vcf" label="${tool.name} on ${on_string}: variants fail" />
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76 <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
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77 <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
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78 <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: coverage mask" />
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79 <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="reference_source_selector" value="history" />
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84 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
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85 <param name="reference" value="nCoV-2019.reference.fasta" />
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86 <param name="primer_scheme_source_selector" value="tool_data_table" />
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87 <param name="primer_scheme_bedfile" value="test_entry" />
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88 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
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89 </test>
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90 <test>
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91 <param name="reference_source_selector" value="history" />
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92 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
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93 <param name="reference" value="nCoV-2019.reference.fasta" />
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94 <param name="primer_scheme_source_selector" value="history" />
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95 <param name="primer_scheme_bedfile" value="nCoV-2019.V1.bed" />
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96 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
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97 </test>
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98 <test>
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99 <param name="reference_source_selector" value="tool_data_table" />
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100 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
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101 <param name="reference" value="test_entry" />
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102 <param name="primer_scheme_source_selector" value="tool_data_table" />
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103 <param name="primer_scheme_bedfile" value="test_entry" />
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104 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 This tool aligns MinION reads that were generated from a tiling amplicon library against a viral reference sequence.
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109 It generates a consensus fasta file and a vcf variant file.
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110
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111 This tool is configured to use the experimental 'medaka' variant caller.
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112 ]]></help>
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113 <citations>
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114 </citations>
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115 </tool>