Mercurial > repos > iuc > mykrobe_predict

annotate macro.xml @ 3:e8405163fb4e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
author iuc
date Tue, 10 Aug 2021 11:29:58 +0000
parents cedd631dc124
children a2e3ad69ee23
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cedd631dc124 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 65f9e423263afc8f23fa51cb4770998b99f933ba"
iuc
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1 <?xml version="1.1"?>
0
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2 <macros>
3
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3 <token name="@TOOL_VERSION@">0.10.0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
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7 </requirements>
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8 </xml>
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9 <token name="@select_inputs@">
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10 <![CDATA[
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11 #set $name='sample'
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12 ]]>
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13 </token>
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14
1
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15 <token name="@shared_options@">
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16 <![CDATA[
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17 #if $kmer:
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18 --kmer '${kmer}'
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19 #end if
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20 #if $expected_depth:
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21 --expected_depth '${expected_depth}'
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22 #end if
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24 $ont
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26 $report_all_calls
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28 #if $expected_error_rate:
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29 --expected_error_rate '${expected_error_rate}'
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30 #end if
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32 #if $min_variant_conf:
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33 --min_variant_conf '${min_variant_conf}'
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34 #end if
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36 #if $min_gene_conf:
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37 --min_gene_conf '${min_gene_conf}'
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38 #end if
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40 #if $min_proportion_expected_depth:
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41 --min_proportion_expected_depth '${min_proportion_expected_depth}'
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42 #end if
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44 #if $min_gene_percent_covg_threshold:
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45 --min_gene_percent_covg_threshold '${min_gene_percent_covg_threshold}'
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46 #end if
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48 $guess_sequence_method
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49
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50 $ignore_minor_calls
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52 #if $ignore_filtered:
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53 --ignore_filtered '${ignore_filtered}'
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54 #end if
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56 #if $model:
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57 --model '${model}'
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58 #end if
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59
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60 #if $ploidy:
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61 --ploidy '${ploidy}'
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62 #end if
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63 ]]>
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64 </token>
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65
0
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66 <xml name="inputs">
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67 <conditional name="data_type">
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68 <param name="type" type="select" label="Specify the read type.">
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69 <option value="single">Single-end Data</option>
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70 <option value="paired">Paired-end Data</option>
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71 <option value="collection">Collection Paired-end Data</option>
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72 </param>
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73 <when value="single">
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74 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
0
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75 </when>
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76 <when value="paired">
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77 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
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78 <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
0
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79 </when>
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80 <when value="collection">
3
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81 <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
0
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82 </when>
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83 </conditional>
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84 </xml>
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85
1
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86 <xml name="options">
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87 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
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88 <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate" help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
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89 <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>
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90 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
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91 <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
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92 <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>
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93 <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage" help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/>
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94 <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
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95 <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
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96 <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
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97 <option value="diploid">diploid</option>
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98 <option value="haploid">haploid</option>
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99 </param>
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100 <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>
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101 <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>
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102 <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
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103 <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method" help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
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104 </xml>
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105
0
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106 <token name="@ATTRIBUTION@">
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107 <![CDATA[
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108
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109 **MyKrobe predict - Antibiotic resistance predictions**
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110
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111 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
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112 using Bruijn graph.
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113 ]]>
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114 </token>
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115
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116 <xml name="citation">
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117 <citations>
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118 <citation type="doi">10.1038/ncomms10063</citation>
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119 </citations>
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120 </xml>
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121 </macros>