Mercurial > repos > iuc > amrfinderplus

annotate amrfinderplus.xml @ 7:7844dbe4f8e2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
author iuc
date Thu, 30 May 2024 13:07:03 +0000
parents 1920244e2895
children
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a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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1 <tool id="amrfinderplus" name="AMRFinderPlus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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2 <description>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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3 NCBI Antimicrobial Resistance Gene Finder
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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4 </description>
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5 <macros>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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6 <import>macro.xml</import>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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7 </macros>
6
1920244e2895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit b9e8ae9eeeff6fb23e25eca3d4a89323c7f37c33
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8 <expand macro="biotools"/>
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a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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9 <expand macro="requirements"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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10 <expand macro="version_command"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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11 <command detect_errors="aggressive"><![CDATA[
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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12 amrfinder
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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13 #*======================================
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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14 CPU option
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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15 ======================================*#
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16 --threads \${GALAXY_SLOTS:-1}
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17 #*======================================
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18 DATABASE
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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19 ======================================*#
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20 --database '$input_option.amrfinder_db_select.fields.path'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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21 #*======================================
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22 INPUT TYPE
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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23 ======================================*#
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24 #if $input_option.input_mode.input_select == 'nucleotide'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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25 --nucleotide $input_option.input_mode.nucleotide_input
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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26 #if $input_option.input_mode.nucleotide_flank5_size > 0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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27 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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28 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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29 #end if
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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30 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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31 #elif $input_option.input_mode.input_select == 'protein'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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32 --protein $input_option.input_mode.protein_input
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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33 #if $input_option.input_mode.gff_annotation
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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34 --gff $input_option.input_mode.gff_annotation
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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35 #end if
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36 #if $input_option.input_mode.annotation_format
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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37 --annotation_format $input_option.input_mode.annotation_format
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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38 #end if
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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39 --protein_output 'amrfinderplus_protein_output.fasta'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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40 #else
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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41 --nucleotide $input_option.input_mode.nucleotide_input
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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42 #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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43 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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44 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
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45 #end if
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46 --protein $input_option.input_mode.protein_input
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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47 --gff $input_option.input_mode.gff_annotation
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48 --annotation_format $input_option.input_mode.annotation_format
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49 --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
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50 --protein_output 'amrfinderplus_protein_output.fasta'
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51 #end if
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52 #*======================================
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53 ORGANISM PART
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54 ======================================*#
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55 #if $organism_options.organism_conditionnal.organism_select
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56 --organism '$organism_options.organism_conditionnal.organism'
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57 #if $organism_options.organism_conditionnal.mutation_all
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58 $organism_options.organism_conditionnal.mutation_all 'mutation_all_report.tsv'
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59 #end if
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60 #if $options.plus
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61 $organism_options.organism_conditionnal.report_common
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62 #end if
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63 #end if
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64 #*======================================
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65 OPTIONS
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66 ======================================*#
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67 --ident_min '$options.ident_min'
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68 --coverage_min '$options.coverage_min'
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69 #if '$options.translation_table'
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70 --translation_table '$options.translation_table'
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71 #end if
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72 #if '$options.name'
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73 --name '$options.name'
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74 #end if
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75 $options.plus
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76 $options.report_all_equal
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77 $options.print_node
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78 --output 'amrfinderplus_report.tsv'
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79
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80 ]]></command>
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81 <inputs>
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82 <!-- DB and file INPUT -->
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83 <section name="input_option" title="Input/Output options" expanded="true">
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84 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
7
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85 <options from_data_table="amrfinderplus_versioned_database">
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86 <filter type="static_value" value="3.12" column="db_version"/>
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87 <validator message="No amrfinderplus database is available" type="no_options"/>
0
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88 </options>
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89 </param>
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90 <conditional name="input_mode">
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91 <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)">
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92 <option value="nucleotide">Nucleotide</option>
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93 <option value="protein">Protein</option>
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94 <option value="nucl_prot">Nucleotide and Protein</option>
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95 </param>
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96 <when value="nucleotide">
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97 <expand macro="nucl_input" option="false"/>
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98 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/>
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99 </when>
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100 <when value="protein">
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101 <expand macro="prot_input" option="false"/>
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102 <expand macro="annotation_type" option="true"/>
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103 </when>
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104 <when value="nucl_prot">
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105 <expand macro="nucl_input" option="false"/>
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106 <expand macro="prot_input" option="false"/>
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107 <expand macro="annotation_type" option="false"/>
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108 <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/>
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109 </when>
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110 </conditional>
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111 </section>
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112 <!-- ORGANISM OPTIONS -->
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113 <section name="organism_options" title="Organism options">
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114 <conditional name="organism_conditionnal">
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115 <param name="organism_select" type="select" label="Add organism specifications">
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116 <option value="" selected="true">No specifications</option>
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117 <option value="add_organism">Add organism specifications</option>
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118 </param>
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119 <when value="add_organism">
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120 <param argument="--organism" type="select" optional="false" label="Taxonomy group point mutation" help="Choose a taxonomic group to point mutation screening">
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121 <option value="Acinetobacter_baumannii">Acinetobacter_baumannii</option>
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122 <option value="Burkholderia_cepacia">Burkholderia_cepacia</option>
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123 <option value="Burkholderia_pseudomallei">Burkholderia_pseudomallei</option>
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124 <option value="Campylobacter">Campylobacter</option>
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125 <option value="Citrobacter_freundii">Citrobacter_freundii</option>
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126 <option value="Clostridioides_difficile">Clostridioides_difficile</option>
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127 <option value="Enterobacter_cloacae">Enterobacter_cloacae</option>
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128 <option value="Enterococcus_faecalis">Enterococcus_faecalis</option>
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129 <option value="Enterococcus_faecium">Enterococcus_faecium</option>
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130 <option value="Escherichia">Escherichia</option>
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131 <option value="Klebsiella_aerogenes">Klebsiella_aerogenes</option>
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132 <option value="Klebsiella_oxytoca">Klebsiella_oxytoca</option>
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133 <option value="Klebsiella_pneumoniae">Klebsiella_pneumoniae</option>
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134 <option value="Neisseria_gonorrhoeae">Neisseria_gonorrhoeae</option>
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135 <option value="Neisseria_meningitidis">Neisseria_meningitidis</option>
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136 <option value="Pseudomonas_aeruginosa">Pseudomonas_aeruginosa</option>
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137 <option value="Salmonella">Salmonella</option>
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138 <option value="Serratia_marcescens">Serratia_marcescens</option>
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139 <option value="Staphylococcus_aureus">Staphylococcus_aureus</option>
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140 <option value="Staphylococcus_pseudintermedius">Staphylococcus_pseudintermedius</option>
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141 <option value="Streptococcus_agalactiae">Streptococcus_agalactiae</option>
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142 <option value="Streptococcus_pneumoniae">Streptococcus_pneumoniae</option>
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143 <option value="Streptococcus_pyogenes">Streptococcus_pyogenes</option>
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144 <option value="Vibrio_cholerae">Vibrio_cholerae</option>
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145 </param>
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146 <param argument="--mutation_all" type="boolean" truevalue="--mutation_all" falsevalue="" label="Report genotypes at all locations screened for point mutations"/>
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147 <param argument="--report_common" type="boolean" truevalue="--report_common" falsevalue=""
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148 label="Report proteins common to a taxonomy group (need the plus and organism options)"/>
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149 </when>
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150 <when value="">
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151 </when>
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152 </conditional>
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153 </section>
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154 <!-- OPTIONS -->
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155 <section name="options" title="Options">
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156 <param argument="--ident_min" type="float" min="-1" max="1" value="-1" label="Minimum identity"
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157 help="Minimum proportion of identical amino acids in alignment. -1 means use a curated threshold if it exists and 0.9 otherwise (default: -1)"/>
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158 <param argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage"
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159 help="Minimum coverage of the reference protein (0 to 1, default: 0.5)"/>
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160 <param argument="--translation_table" type="select" optional="true" label="Translation table" help="NCBI genetic code for translated BLAST (default: bacterial table 11)">
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161 <option value="1">1 Standard code</option>
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162 <option value="2">2 Vertebrate mitochondrial</option>
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163 <option value="3">3 Yeast mitochondrial</option>
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164 <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
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165 <option value="5">5 Invertebrate mitochondrial</option>
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166 <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
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167 <option value="9">9 Echinoderm and flatworm mitochondrial</option>
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168 <option value="10">10 Euplotid nuclear</option>
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169 <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
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170 <option value="12">12 Alternative yeast nuclear</option>
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171 <option value="13">13 Ascidian mitochondrial</option>
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172 <option value="14">14 Alternative flatworm mitochondrial</option>
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173 <option value="16">16 Chlorophycean mitochondrial</option>
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174 <option value="21">21 Trematode Mitochondrial</option>
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175 <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
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176 <option value="23">23 Thraustochytrium Mitochondrial</option>
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177 <option value="24">24 Rhabdopleuridae Mitochondrial</option>
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178 <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
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179 <option value="26">26 Pachysolen tannophilus Nuclear</option>
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180 <option value="27">27 Karyorelict Nuclear</option>
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181 <option value="28">28 Condylostoma Nuclear</option>
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182 <option value="29">29 Mesodinium nuclear</option>
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183 <option value="30">30 Peritrich nuclear</option>
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184 <option value="31">31 Blastocrithidia nuclear</option>
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185 <option value="33">33 Cephalodiscidae mitochondrial</option>
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186 </param>
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187 <param argument="--plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report"/>
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188 <param argument="--report_all_equal" type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/>
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189 <param argument="--print_node" type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/>
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190 <param argument="--name" type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/>
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191 </section>
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192 </inputs>
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193 <outputs>
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194 <data name="amrfinderplus_report" format="tabular" from_work_dir="amrfinderplus_report.tsv" label="${tool.name} on ${on_string}: AMRFinderPlus report"/>
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195 <data name="mutation_all_report" format="tabular" from_work_dir="mutation_all_report.tsv" label="${tool.name} on ${on_string}: Point mutation report">
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196 <filter> organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True </filter>
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197 </data>
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198 <data name="protein_output" format="fasta" from_work_dir="amrfinderplus_protein_output.fasta" label="${tool.name} on ${on_string}: Protein identified sequences">
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199 <filter> input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']</filter>
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200 </data>
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201 <data name="nucleotide_output" format="fasta" from_work_dir="amrfinderplus_nucleotide_output.fasta" label="${tool.name} on ${on_string}: Nucleotide identified sequences">
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202 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] </filter>
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203 </data>
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204 <data name="nucleotide_flank5_output" format="fasta" from_work_dir="amrfinderplus_flanking_sequence_output.fasta"
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205 label="${tool.name} on ${on_string}: Nucleotide sequences with 5' flanking regions">
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206 <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and input_option['input_mode']['nucleotide_flank5_size'] != 0 </filter>
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207 </data>
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208 </outputs>
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209 <tests>
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210 <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input -->
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211 <section name="input_option">
7
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212 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
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213 <conditional name="input_mode">
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214 <param name="input_select" value="nucleotide"/>
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215 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
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216 </conditional>
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217 </section>
7
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218 <output name="amrfinderplus_report" ftype="tabular">
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219 <assert_contents>
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220 <has_n_columns n="22"/>
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221 <has_n_lines n="8"/>
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222 <has_text text="optrA"/>
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223 <has_text text="WP_063854496"/>
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224 <has_text text="WP_063843211"/>
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225 </assert_contents>
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226 </output>
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227 <output name="nucleotide_output" ftype="fasta">
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228 <assert_contents>
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229 <has_n_lines n="142"/>
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230 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
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231 <has_text text="TTGTCCAAAGCC"/>
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232 </assert_contents>
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233 </output>
0
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234 </test>
1
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235 <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options -->
0
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236 <section name="input_option">
7
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237 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
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238 <conditional name="input_mode">
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239 <param name="input_select" value="nucleotide"/>
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240 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
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241 <param name="nucleotide_flank5_size" value="150"/>
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242 </conditional>
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243 </section>
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244 <section name="organism_options">
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245 <conditional name="organism_conditionnal">
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246 <param name="organism_select" value="add_organism"/>
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247 <param name="organism" value="Enterococcus_faecalis"/>
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248 <param name="report_common" value="true"/>
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249 </conditional>
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250 </section>
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251 <section name="options">
7
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252 <param name="ident_min" value="0.1"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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253 <param name="coverage_min" value="0.1"/>
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254 <param name="translation_table" value="11"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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255 <param name="plus" value="true"/>
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256 <param name="report_all_equal" value="true"/>
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257 <param name="print_node" value="true"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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258 <param name="name" value="test_2"/>
7
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259 <param name="log" value="true"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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260 </section>
7
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261 <output name="amrfinderplus_report" ftype="tabular">
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262 <assert_contents>
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263 <has_n_columns n="24"/>
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264 <has_n_lines n="13"/>
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265 <has_text text="optrA"/>
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266 <has_text text="WP_063854496"/>
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267 </assert_contents>
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268 </output>
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269 <output name="nucleotide_output" ftype="fasta">
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270 <assert_contents>
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271 <has_n_lines n="267"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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272 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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273 <has_text text="TTGTCCAAAGCC"/>
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274 </assert_contents>
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275 </output>
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276 <output name="nucleotide_flank5_output" ftype="fasta">
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277 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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278 <has_n_lines n="298"/>
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279 <has_text text=">contig_2:54987-57395 strand:- mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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280 <has_text text="TTGTCCAAAGCC"/>
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281 </assert_contents>
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282 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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283 </test>
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284 <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options -->
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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285 <section name="input_option">
7
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286 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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287 <conditional name="input_mode">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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288 <param name="input_select" value="nucleotide"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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289 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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290 </conditional>
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291 </section>
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292 <section name="organism_options">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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293 <conditional name="organism_conditionnal">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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294 <param name="organism_select" value="add_organism"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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295 <param name="organism" value="Enterococcus_faecalis"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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296 <param name="report_common" value="true"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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297 </conditional>
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298 </section>
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299 <section name="options">
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300 <param name="report_all_equal" value="true"/>
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301 </section>
7
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302 <output name="amrfinderplus_report" ftype="tabular">
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303 <assert_contents>
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304 <has_n_columns n="22"/>
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305 <has_n_lines n="9"/>
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diff changeset
306 <has_text text="optrA"/>
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307 <has_text text="WP_063854496"/>
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diff changeset
308 <has_text text="WP_063856080"/>
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309 </assert_contents>
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310 </output>
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311 <output name="nucleotide_output" ftype="fasta">
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312 <assert_contents>
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313 <has_n_lines n="142"/>
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314 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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diff changeset
315 <has_text text="TTGTCCAAAGCC"/>
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316 </assert_contents>
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317 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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318 </test>
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319 <test expect_num_outputs="2"> <!-- TEST_4 simple protein input -->
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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320 <section name="input_option">
7
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diff changeset
321 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
322 <conditional name="input_mode">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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diff changeset
323 <param name="input_select" value="protein"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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324 <param name="protein_input" value="enterococcus_faecalis.faa"/>
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325 </conditional>
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diff changeset
326 </section>
7
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diff changeset
327 <output name="amrfinderplus_report" ftype="tabular">
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diff changeset
328 <assert_contents>
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iuc
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diff changeset
329 <has_n_columns n="18"/>
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diff changeset
330 <has_n_lines n="7"/>
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iuc
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diff changeset
331 <has_text text="optrA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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diff changeset
332 <has_text text="WP_063854496"/>
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iuc
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diff changeset
333 <has_text text="WP_063856080"/>
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diff changeset
334 </assert_contents>
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diff changeset
335 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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336 <output name="protein_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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337 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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338 <has_n_lines n="49"/>
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339 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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340 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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341 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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342 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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343 </test>
1
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iuc
parents: 0
diff changeset
344 <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta -->
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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345 <section name="input_option">
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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346 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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347 <conditional name="input_mode">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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348 <param name="input_select" value="protein"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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349 <param name="protein_input" value="enterococcus_faecalis.faa"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
350 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
351 <param name="annotation_format" value="bakta"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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352 </conditional>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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diff changeset
353 </section>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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354 <section name="organism_options">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
355 <conditional name="organism_conditionnal">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
356 <param name="organism_select" value="add_organism"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
357 <param name="organism" value="Enterococcus_faecalis"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
358 <param name="report_common" value="true"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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diff changeset
359 </conditional>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
360 </section>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
361 <section name="options">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
362 <param name="ident_min" value="0.1"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
363 <param name="coverage_min" value="0.4"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
364 <param name="translation_table" value="11"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
365 <param name="plus" value="true"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
366 <param name="report_all_equal" value="true"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
367 <param name="print_node" value="true"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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diff changeset
368 <param name="name" value="test_5"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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diff changeset
369 </section>
7
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diff changeset
370 <output name="amrfinderplus_report" ftype="tabular">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
371 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
372 <has_n_columns n="24"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
373 <has_n_lines n="8"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
374 <has_text text="optrA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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diff changeset
375 <has_text text="IDOBJL_14770"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
376 <has_text text="WP_063856080"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
377 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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diff changeset
378 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
379 <output name="nucleotide_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
380 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
381 <has_n_lines n="49"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
382 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
383 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
384 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
385 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
386 </test>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
387 <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation -->
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
388 <section name="input_option">
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
389 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
390 <conditional name="input_mode">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
391 <param name="input_select" value="protein"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
392 <param name="protein_input" value="PROKKA_05252023.faa"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
393 <param name="gff_annotation" value="PROKKA_05252023.gff"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
394 <param name="annotation_format" value="prokka"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
395 </conditional>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
396 </section>
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
397 <output name="amrfinderplus_report" ftype="tabular">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
398 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
399 <has_n_columns n="22"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
400 <has_n_lines n="7"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
401 <has_text text="FODBOAIN_02586"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
402 <has_text text="WP_063856395"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
403 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
404 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
405 <output name="protein_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
406 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
407 <has_n_lines n="49"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
408 <has_text text=">FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
409 <has_text text="YSNLLLLFSGIIVISWLVTLNVYKHSQRDF"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
410 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
411 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
412 </test>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
413 <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation -->
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
414 <section name="input_option">
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
415 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
416 <conditional name="input_mode">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
417 <param name="input_select" value="protein"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
418 <param name="protein_input" value="input_ncbi.faa"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
419 <param name="gff_annotation" value="annotation_ncbi.gff3"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
420 </conditional>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
421 </section>
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
422 <output name="amrfinderplus_report" ftype="tabular">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
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423 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
424 <has_n_columns n="22"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
425 <has_n_lines n="4"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
426 <has_text text="blaOXA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
427 <has_text text="WP_063855540"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
428 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
429 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
430 <output name="protein_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
431 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
432 <has_n_lines n="17"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
433 <has_text text=">blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
434 <has_text text="SSNPDAAPVSS"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
435 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
436 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
437 </test>
1
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
438 <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input -->
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
439 <section name="input_option">
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
440 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
441 <conditional name="input_mode">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
442 <param name="input_select" value="nucl_prot"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
443 <param name="protein_input" value="enterococcus_faecalis.faa"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
444 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
445 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
446 <param name="annotation_format" value="bakta"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
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diff changeset
447 </conditional>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
448 </section>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
449 <section name="organism_options">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
450 <conditional name="organism_conditionnal">
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
451 <param name="organism_select" value="add_organism"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
452 <param name="organism" value="Enterococcus_faecalis"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
453 </conditional>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
454 </section>
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
455 <output name="amrfinderplus_report" ftype="tabular">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
456 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
457 <has_n_columns n="22"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
458 <has_n_lines n="8"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
459 <has_text text="IDOBJL_14770"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
460 <has_text text="WP_063856080"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
461 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
462 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
463 <output name="nucleotide_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
464 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
465 <has_n_lines n="143"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
466 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
467 <has_text text="CTTATCTGTATAG"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
468 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
469 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
470 <output name="protein_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
471 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
472 <has_n_lines n="37"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
473 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
474 <has_text text="QEAGAGMSLLNFT"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
475 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
476 </output>
1
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
477 </test>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
478 <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results -->
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
479 <section name="input_option">
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
480 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
1
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
481 <conditional name="input_mode">
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
482 <param name="input_select" value="nucl_prot"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
483 <param name="protein_input" value="e_faecalis_rast.faa"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
484 <param name="nucleotide_input" value="e_faecalis_rast.fna"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
485 <param name="gff_annotation" value="e_faecalis_rast.gff"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
486 <param name="annotation_format" value="rast"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
487 </conditional>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
488 </section>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
489 <section name="organism_options">
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
490 <conditional name="organism_conditionnal">
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
491 <param name="organism_select" value="add_organism"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
492 <param name="organism" value="Enterococcus_faecalis"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
493 <param name="mutation_all" value="true"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
494 </conditional>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
495 </section>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
496 <section name="options">
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iuc
parents: 0
diff changeset
497 <param name="ident_min" value="0.1"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
498 <param name="coverage_min" value="0.1"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
499 <param name="plus" value="true"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
500 <param name="print_node" value="true"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
501 <param name="name" value="test_5"/>
a37bb163d05d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
iuc
parents: 0
diff changeset
502 </section>
7
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
503 <output name="amrfinderplus_report" ftype="tabular">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
504 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
505 <has_n_columns n="24"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
506 <has_n_lines n="2"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
507 <has_text text="MUPIROCIN"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
508 <has_text text="WP_063854488"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
509 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
510 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
511 <output name="nucleotide_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
512 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
513 <has_n_lines n="40"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
514 <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
515 <has_text text="ATCAGTCGTGAAATAGAA"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
516 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
517 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
518 <output name="protein_output" ftype="fasta">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
519 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
520 <has_n_lines n="0"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
521 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
522 </output>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
523 <output name="mutation_all_report" ftype="tabular">
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
524 <assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
525 <has_n_columns n="24"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
526 <has_n_lines n="5"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
527 <has_text text="23S_GA375AG"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
528 <has_text text="NZ_CP04"/>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
529 </assert_contents>
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents: 6
diff changeset
530 </output>
0
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
531 </test>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
532 </tests>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
533 <help><![CDATA[
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
534 **What it does**
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
535
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
536 AMRFinderPlus is a tool to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
537
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
538 **Input file analysis**
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
539
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
540 AMRFinderPlus can check in nucleotide and/or protein fasta file
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
541 When protein file is provided, sensitivity is higher if you add an annotation file
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
542
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
543 **Organism options**
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
544
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
545 With organism informations AMRFinderPlus screens known resistance causing point mutations and blacklisting of common, non-informative genes.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
546
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
547 The **mutation_all** option make a new output file containing all detected variants from the reference sequence.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
548
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
549 This file allows you to distinguish between called point mutations that were the sensitive variant and the point mutations that could not be called because the sequence was not found.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
550
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
551 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
552 | Organism option | Point mutations | Blacklisted plus genes | Notes |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
553 +=================================+==================+=============================+============================================================+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
554 | Acinetobacter_baumannii | X | | Use for the A. baumannii-calcoaceticus species complex |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
555 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
556 | Burkholderia_cepacia | X | | Use for the Burkholderia cepacia species complex |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
557 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
558 | Burkholderia_pseudomallei | X | | Use for the Burkholderia pseudomallei species complex |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
559 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
560 | Campylobacter | X | | Use for C. coli and C. jejuni |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
561 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
562 | Citrobacter_freundii | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
563 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
564 | Clostridioides_difficile | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
565 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
566 | Enterobacter_cloacae | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
567 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
568 | Enterococcus_faecalis | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
569 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
570 | Enterococcus_faecium | X | | Use for E. hirae |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
571 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
572 | Escherichia | X | X | Use for Shigella and Escherichia |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
573 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
574 | Klebsiella_oxytoca | X | X | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
575 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
576 | Klebsiella_pneumoniae | X | X | Use for K. pneumoniae species complex and K. aerogenes |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
577 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
578 | Neisseria_gonorrhoeae | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
579 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
580 | Neisseria_meningitidis | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
581 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
582 | Pseudomonas_aeruginosa | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
583 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
584 | Salmonella | X | X | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
585 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
586 | Serratia_marcescens | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
587 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
588 | Staphylococcus_aureus | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
589 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
590 | Staphylococcus_pseudintermedius | X | X | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
591 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
592 | Streptococcus_agalactiae | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
593 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
594 | Streptococcus_pneumoniae | X | | Use for S. pneumoniae and S. mitis |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
595 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
iuc
parents:
diff changeset
596 | Streptococcus_pyogenes | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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597 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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598 | Vibrio_cholerae | X | | |
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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599 +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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600
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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601
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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602 **Supplementary options**
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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603 - *nucleotide 5' flanking size* to extract nucleotide matches and a range of nucleotide in 5'
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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604 - *Minimum identity* to choose threshold in amino acids alignemnt. -1 for a high curation threshold.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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605 - *Minimum coverage* Coverage to protein alignment.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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606 - *Translation table* by default AMRFinderPlus work on bacteria but can be modified to some other Phyla.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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607 - *Plus* option provide more information related to virulence, stress response ...
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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608
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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609 **Output files**
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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610
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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611 AMRFinderPlus can generate some differents files :
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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612 - The AMRFinderPlus report with identified protein, gene and AMR related informations.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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613 - A report with all detected variants from the reference sequence.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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614 - The protein and/ort nucleotide matched sequences.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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615 - Only when nucleotide a nucleotide fasta file could be provided with 5' flanking regions.
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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616
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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617
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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618 ]]></help>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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619 <expand macro="citations"/>
a968af0a91f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 73f592a7f1c1e9577bbf56a1347bd5c01bb8ea14
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620 </tool>