Mercurial > repos > iuc > artic_minion

annotate artic_minion.xml @ 8:6f52ebc01098 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 42a048391200da4c664650f7e7665c97ace584ee"
author iuc
date Mon, 07 Feb 2022 09:41:30 +0000
parents f5643712dca7
children
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1 <tool id="artic_minion" name="ARTIC minion" version="@PACKAGE_VERSION@+galaxy0" profile="20.09">
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2 <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6
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6 <xrefs>
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7 <xref type="bio.tools">artic</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 mkdir -p 'scheme/name/V1' &&
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14 #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
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15 ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/V1/name.scheme.bed' &&
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16 #else:
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17 ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/V1/name.scheme.bed' &&
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18 #end if
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19 #if str( $reference_source.reference_source_selector ) == "history":
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20 ln -s '${reference_source.reference}' 'scheme/name/V1/name.reference.fasta' &&
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21 samtools faidx 'scheme/name/V1/name.reference.fasta' &&
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22 #else:
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23 ln -s '${reference_source.reference.fields.path}' 'scheme/name/V1/name.reference.fasta' &&
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24 samtools faidx 'scheme/name/V1/name.reference.fasta' &&
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25 #end if
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26 artic minion
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27 --threads \${GALAXY_SLOTS:-1}
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28 #if $normalise > 0:
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29 --normalise ${normalise}
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30 #end if
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31 --read-file '${read_file}'
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32 --scheme-directory 'scheme'
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33 --medaka
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34 --medaka-model '$medaka_model'
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35 $bwa
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36 'name/V1'
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37 ## enclose the sample name in extra single quotes because
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38 ## the minion pipeline script doesn't care about passing
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39 ## its arguments safely.
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40 "'"'${read_file.element_identifier}'"'"
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41 && bgzip -f '${read_file.element_identifier}.fail.vcf'
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42 ## remove enclosing single-quotes from header of output consensus fasta
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43 && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" '${read_file.element_identifier}.consensus.fasta'
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44 ]]></command>
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45 <inputs>
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46 <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
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47 <param argument="--normalise" type="integer" min="0" value="0"
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48 label="Coverage normalisation depth"
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49 help="Sample at most this number of reads per amplicon and strand. default=0 (use all reads)" />
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50 <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
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51 <conditional name="primer_scheme_source">
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52 <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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53 help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
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54 <option value="tool_data_table">From tool data table</option>
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55 <option value="history">From history</option>
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56 </param>
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57 <when value="tool_data_table">
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58 <param name="primer_scheme_bedfile" type="select" format="tabular" label="Primer Scheme">
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59 <options from_data_table="primer_scheme_bedfiles">
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60 <validator type="no_options" message="No primer scheme .bed files 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="primer_scheme_bedfile" type="data" format="tabular" label="Primer Scheme" />
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66 </when>
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67 </conditional>
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68 <conditional name="reference_source">
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69 <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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70 <option value="cached">Use a built-in reference</option>
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71 <option value="history">Use a reference from history</option>
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72 </param>
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73 <when value="cached">
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74 <param name="reference" type="select" label="Using reference genome" help="Select genome from the list">
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75 <options from_data_table="all_fasta">
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76 <filter type="sort_by" column="2" />
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77 <validator type="no_options" message="No references are available" />
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78 </options>
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79 </param>
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80 </when>
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81 <when value="history">
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82 <param name="reference" type="data" format="fasta" label="Use the following dataset as the reference sequence"
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83 help="You can upload a FASTA sequence to the history and use it as reference" />
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84 </when>
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85 </conditional>
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86 <param type="text" name="medaka_model" label="Medaka model" help="Model string to pass to medaka (see https://github.com/nanoporetech/medaka#models)">
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87 <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>
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88 </param>
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89 </inputs>
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90 <outputs>
3
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91 <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
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92 <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
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93 <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: medaka variant calls" />
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94 <data name="variants_fail_vcf" format="vcf_bgzip" from_work_dir="*.fail.vcf.gz" label="${tool.name} on ${on_string}: variants fail" />
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95 <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${tool.name} on ${on_string}: variants pass" />
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96 <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
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97 <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: consensus coverage mask" />
1
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98 <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
0
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="reference_source_selector" value="history" />
1
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103 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
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104 <param name="reference" value="nCoV-2019.reference.fasta" />
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105 <param name="primer_scheme_source_selector" value="tool_data_table" />
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106 <param name="primer_scheme_bedfile" value="test_entry" />
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107 <param name="medaka_model" value="r941_min_high_g360" />
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108 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
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109 </test>
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110 <test>
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111 <param name="reference_source_selector" value="history" />
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112 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
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113 <param name="reference" value="nCoV-2019.reference.fasta" />
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114 <param name="primer_scheme_source_selector" value="history" />
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115 <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.V1.bed" />
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116 <param name="medaka_model" value="r941_min_high_g360" />
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117 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
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118 </test>
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119 <test>
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120 <param name="reference_source_selector" value="tool_data_table" />
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121 <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
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122 <param name="reference" value="test_entry" />
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123 <param name="primer_scheme_source_selector" value="tool_data_table" />
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124 <param name="primer_scheme_bedfile" value="test_entry" />
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125 <param name="medaka_model" value="r941_min_high_g360" />
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126 <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
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127 </test>
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128 </tests>
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129 <help><![CDATA[
5
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130 ARTIC_ minion aligns Nanopore reads that were generated from a tiling amplicon library against a viral reference sequence.
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131 It generates a consensus fasta file and a vcf variant file.
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132
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133 This tool is configured to use the experimental 'medaka' variant caller and must be supplied with the name of
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134 a model file to use with 'medaka', see the `medaka web page`_ for details.
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135
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136 .. _ARTIC: https://artic.readthedocs.io/en/latest/
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137 .. _medaka web page: https://github.com/nanoporetech/medaka#models
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138
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139 Note that you should choose an appropriate model for the medaka version used by ARTIC minion.
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140
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141 ================== ==================
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142 ARTIC version medaka version
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143 ================== ==================
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144 1.2.1 1.0.3
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145 1.3.0-dev 1.2.3
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146 ================== ==================
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147 ]]></help>
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148 <expand macro="citations" />
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149 </tool>