Mercurial > repos > iuc > mykrobe_predict

annotate mykrobe_predict.xml @ 0:33463c79e697 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
author iuc
date Sat, 13 Jan 2018 09:02:31 -0500
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33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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1 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.5.6" >
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2 <description>Antibiotic resistance predictions</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 @select_inputs@
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11 mykrobe predict
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12 '$name'
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13 $select_species.species
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16 #if $select_species.species =='tb':
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17 --panel $select_species.panel
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18 #end if
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22 #if $kmer:
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23 --kmer $kmer
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24 #end if
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26 #if $min_variant_conf:
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27 --min_variant_conf $min_variant_conf
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28 #end if
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31 #if $expected_depth:
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32 --expected_depth $expected_depth
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33 #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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42 #if $min_gene_percent_covg_threshold:
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43 --min_gene_percent_covg_threshold $min_gene_percent_covg_threshold
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44 #end if
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47 #if $min_depth:
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48 --min_depth $min_depth
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49 #end if
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52 #if $expected_error_rate:
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53 --expected_error_rate $expected_error_rate
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54 #end if
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56 $report_all_calls
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58 $ont
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59 -q
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60 -t "\${GALAXY_SLOTS:-1}"
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61
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62 -1
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63 #if $type == 'fastq':
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64 *.fastq
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65 #else
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66 *.bam
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67 #end if
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68 > $json
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69 ]]>
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70 </command>
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71 <inputs>
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72 <expand macro="inputs" />
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73 <conditional name="select_species">
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74 <param name="species" type="select" label="Specify Species for AMR">
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75 <option value="tb">Mycobacterium tuberculosis (tb)</option>
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76 <option value="staph">Staphylococcus aureus (staph)</option>
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77 </param>
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78 <when value="staph"/>
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79 <when value="tb">
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80 <param name="panel" type="select" label="Select panel for TB only">
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81 <option value="bradley-2015">Bradely 2015</option>
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82 <option value="walker-2015">Walker 2015</option>
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83 </param>
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84 </when>
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85 </conditional>
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86 <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
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87 <param name="expected_error_rate" 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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88 <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth" help=""/>
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89 <param name="min_depth" argument="--min_depth" optional="True" type="integer" min="0" label="Minimum Depth" help=""/>
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90 <param name="report_all_calls" argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="report all calls" help=""/>
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91 <param name="ont" argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
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92 <param name="min_variant_conf" argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
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93 <param name="min_gene_conf" argument="--min_gene_conf" optional="True" type="integer" min="0" label="minimum genotype confidence for gene genotyping" help=""/>
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94 <param name="min_gene_percent_covg_threshold" 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 allelesreported))"/>
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95 </inputs>
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96
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97 <outputs>
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98 <data name="json" format="json" label="JSON prediction"/>
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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="type" value="single"/>
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103 <param name="fastq_input1" value="reads.fastq"/>
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104 <param name="species" value="tb"/>
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105 <param name="panel" value="bradley-2015"/>
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106 <output name="json">
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107 <assert_contents>
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108 <has_text_matching expression="variant_calls"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112 </tests>
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113 <help>
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114 @ATTRIBUTION@
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115 </help>
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116 <expand macro="citation" />
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117 </tool>