Mercurial > repos > iuc > metasbt_index

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 92f047d518d90d1a296747511277f397224f4c60
author iuc
date Mon, 25 Aug 2025 20:30:57 +0000
parents 47189346d00d
children
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47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
iuc
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1 <?xml version="1.0"?>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
iuc
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2 <tool name="index" id="metasbt_index" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="@PROFILE@" license="MIT">
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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3 <description>genomes with Sequence Bloom Trees or update an existing database</description>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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4
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5 <macros>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
iuc
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6 <import>macros.xml</import>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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7 </macros>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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8 <expand macro="creator"/>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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9 <expand macro="requirements"/>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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10
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11 <command detect_errors="exit_code"><![CDATA[
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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12 #set input_dir = "./genomes"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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14 mkdir -p "${input_dir}" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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16 #for $genome in $genomes:
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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17 genome_name="\$(echo '${genome.element_identifier}' | sed 's/[^[:alnum:]_.-]/_/g')" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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18 target_fna="${input_dir}/\${genome_name}.fna" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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20 #if $genome.ext.endswith("gz"):
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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21 gzip -dc '${genome}' > "\${target_fna}" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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22 #else
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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23 ln -s '${genome}' "\${target_fna}" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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24 #end if
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26 echo -e "\${target_fna}" >> "./genomes.txt" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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27 #end for
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29 #if $advanced.index_update_conditional.index_update_option == "false":
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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30 while IFS=$'\t' read -r genome_name genome_taxonomy; do
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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31 genome_name="\$(echo '\${genome_name}' | sed 's/[^[:alnum:]_.-]/_/g')" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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32 genome_taxonomy="\$(echo '\${genome_taxonomy}' | sed 's/[^[:alnum:]_.-|]/_/g')" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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34 if [ -f "${input_dir}/\${genome_name}.fna" ]; then
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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35 echo -e "${input_dir}/\${genome_name}.fna\t\${genome_taxonomy}" >> "${input_dir}/genomes.tsv";
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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36 fi
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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37 done < '${taxonomies}' &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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38
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39 metasbt index --workdir "."
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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40 --database "Database"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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41 --references "${input_dir}/genomes.tsv"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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42 --nproc "\${GALAXY_SLOTS:-4}"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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43 --pack
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45 #if $advanced.index_update_conditional.bfs_selection.bfs_auto == "false":
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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46 --filter-size '${advanced.index_update_conditional.bfs_selection.bfs_size}'
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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47 #else:
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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48 --increase-filter-size '${advanced.index_update_conditional.bfs_selection.bfs_size_increase}'
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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49 --min-kmer-occurrences '${advanced.index_update_conditional.bfs_selection.min_kmer_occurrences}'
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50 #end if
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51
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52 #if $advanced.index_update_conditional.kmers_selection.kmers_auto == "false":
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53 --kmer-size '${advanced.index_update_conditional.kmers_selection.kmer_len}'
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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54 #else:
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55 --limit-kmer-size '${advanced.index_update_conditional.kmers_selection.max_kmer_len}'
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56 #end if
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57
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58 #if $advanced.dereplication_selection.dereplication == "true":
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59 --dereplicate '${advanced.dereplication_update_conditional.distance_threshold}'
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60 #end if
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61
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62 #if $advanced.quality_control_selection.quality_control == "true":
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63 --completeness '${advanced.quality_control_selection.completeness}'
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64 --contamination '${advanced.quality_control_selection.contamination}'
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65 #end if
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66
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67 &&
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68 #else:
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69 #if $advanced.index_update_conditional.database_selection.source == "cvmfs":
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70 ln -s '${advanced.index_update_conditional.database_selection.db_tarball.fields.path}' "./MetaSBT-Database.tar.gz" &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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71 #else:
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72 ln -s '${advanced.index_update_conditional.database_selection.db_tarball}' "./MetaSBT-Database.tar.gz" &&
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73 #end if
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74
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75 metasbt unpack --workdir "."
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76 --database "Database"
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77 --tarball "./MetaSBT-Database.tar.gz" &&
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78
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79 rm "./MetaSBT-Database.tar.gz" &&
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80
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81 metasbt update --workdir "."
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82 --database "Database"
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83 --genomes "./genomes.txt"
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84 --nproc "\${GALAXY_SLOTS:-4}"
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85 --pack
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86
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87 #if $advanced.dereplication_selection.dereplication == "true":
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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88 --dereplicate '${advanced.dereplication_selection.distance_threshold}'
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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89 #end if
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90
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91 #if $advanced.quality_control_selection.quality_control == "true":
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92 --completeness '${advanced.quality_control_selection.completeness}'
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93 --contamination '${advanced.quality_control_selection.contamination}'
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94 #end if
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95
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96 &&
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97 #end if
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98
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99 tail -n +3 "./Database/clusters.tsv" > clusters.tsv &&
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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100 tail -n +3 "./Database/genomes.tsv" > genomes.tsv &&
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101
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102 mv ./MetaSBT-Database*.tar.gz MetaSBT-Database.tar.gz
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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103 ]]></command>
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104
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105 <inputs>
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106 <!-- Input genomes -->
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107 <param name="genomes" format="fasta,fasta.gz" multiple="true" type="data"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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108 label="Input genomes"
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109 help="Select a set of input genomes." />
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110
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111 <!-- Optional file with mapping betweek input file names and their taxonomic label -->
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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112 <param name="taxonomies" format="tsv" multiple="false" type="data" optional="true"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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113 label="Input table with taxonomic labels"
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114 help="Optional two-columns table with the input file names and their full taxonomic labels. This is not required in case the input files are not reference genomes." />
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115
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116 <!-- Advanced options -->
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117 <section name="advanced" expanded="true"
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118 title="Advanced options"
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119 help="Access advanced options to customize k-mer length, bloom filter size, and other settings.">
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120
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121 <!-- Show different options in case of index or update -->
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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122 <conditional name="index_update_conditional">
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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123 <param name="index_update_option" type="select"
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124 label="MetaSBT database"
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125 help="When enabled, most of the advanced options are inherited from an already existing database and cannot be modified.">
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126 <option value="true">Update a MetaSBT database</option>
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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127 <option value="false" selected="true">Build your own MetaSBT database from scratch</option>
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128 </param>
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129
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130 <when value="false">
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131 <!-- Index -->
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132 <!-- Estimate a k-mer length -->
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133 <conditional name="kmers_selection">
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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134 <!-- Enable k-mer length estimation -->
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135 <param name="kmers_auto" type="select"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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136 label="K-mer length"
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137 help="Automatically estimate a proper k-mer length for the input set of genomes with Kitsune.">
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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138 <option value="true" selected="true">Estimate a proper k-mer length for your set of genomes</option>
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139 <option value="false">Set a k-mer length</option>
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140 </param>
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141
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142 <when value="true">
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143 <!-- Limit k-mer length -->
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144 <param name="max_kmer_len" type="integer" value="9" min="8" max="128"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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145 label="Max k-mer length"
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146 help="Limit the length of k-mers for the estimation of the best k-mer length with Kitsune." />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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147 </when>
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148
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149 <when value="false">
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150 <!-- K-mer length -->
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151 <param name="kmer_len" type="integer" value="21" min="8" max="128"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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152 label="Set a k-mer length"
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153 help="Set the length of k-mers." />
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154 </when>
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155 </conditional>
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156
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157 <!-- Estimate the bloom filter size -->
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158 <conditional name="bfs_selection">
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159 <!-- Enable bloom filter size estimation -->
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160 <param name="bfs_auto" type="select"
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161 label="Bloom filter size"
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162 help="Automatically estimate the most appropriate bloom filter size that better fits with the input set of genomes with ntCard.">
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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163 <option value="true" selected="true">Estimate the bloom filter size</option>
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164 <option value="false">Set a bloom filter size</option>
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165 </param>
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166
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167 <when value="true">
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168 <!-- Increment the estimated bloom filter size -->
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169 <param name="bfs_size_increase" type="float" value="5" min="0" max="100"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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170 label="Increment the bloom filter size"
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171 help="Increment the estimated bloom filter size by this percentage in case you are planning to update the database with new genomes in future." />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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172
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173 <!-- Minimum number of occurrences of k-mers computed with ntCard -->
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174 <param name="min_kmer_occurrences" type="integer" value="1" min="1"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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175 label="Minimum k-mer occurrences"
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176 help="Minimum number of occurrences of k-mers to be considered for the estimation of the bloom filter size and for building the bloom filter sketches." />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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177 </when>
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178
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179 <when value="false">
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180 <!-- Bloom filter size -->
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181 <param name="bfs_size" type="integer" value="10000"
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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182 label="Set a bloom filter size"
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183 help="Set a bloom filter size for building genome or sequence sketches." />
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184 </when>
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185 </conditional>
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186 </when>
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187
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188 <when value="true">
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189 <expand macro="database"/>
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190 </when>
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191 </conditional>
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192
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193 <conditional name="dereplication_selection">
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194 <!-- Enable the dereplication of input genomes -->
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195 <param name="dereplication" type="select"
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196 label="Dereplication"
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197 help="Enable the dereplication of input genomes based on their ANI distance.">
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198 <option value="true">Dereplicate the input genomes</option>
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199 <option value="false" selected="true">Do not dereplicate the input genomes</option>
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200 </param>
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201
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202 <when value="true">
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203 <!-- ANI distance threshold -->
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204 <param name="distance_threshold" type="float" value="0.01" min="0.0" max="1.0"
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205 label="Distance threshold"
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206 help="Set a threshold based on the ANI distance of the sketch representation of the input genomes versus themselves and the other genomes in the database (in case of an update)." />
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207 </when>
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208
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209 <when value="false" />
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210 </conditional>
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211
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212 <conditional name="quality_control_selection">
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213 <!-- Enable the quality control of input genomes -->
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214 <param name="quality_control" type="select"
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215 label="Quality Control"
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216 help="Filter out genomes based on their completeness and contamination.">
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217 <option value="true">Enable the quality control of input genomes</option>
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218 <option value="false" selected="true">Do not assess for the quality of genomes</option>
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219 </param>
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220
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221 <when value="true">
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222 <!-- Completeness -->
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223 <param name="completeness" type="float" value="90.0" min="0.0" max="100.0"
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224 label="Completeness threshold"
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225 help="Set a threshold on the completeness and discard everything below this threshold." />
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226
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227 <!-- Contamination -->
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228 <param name="contamination" type="float" value="5.0" min="0.0" max="100.0"
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229 label="Contamination threshold"
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230 help="Set a threshold on the contamination and discard everything above this threshold." />
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231 </when>
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232
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233 <when value="false" />
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234 </conditional>
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235 </section>
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236 </inputs>
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237
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238 <outputs>
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239 <!-- Table with known and unknown clusters -->
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240 <data format="tabular" name="clusters_table" label="${tool.name} on ${on_string}: clusters" from_work_dir="clusters.tsv">
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241 <actions>
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242 <action name="column_names" type="metadata" default="Cluster,Level,Bloom Filter Density,Number of Reference Genomes,Number of MAGs,List of Reference Genomes,List of MAGs,Cluster Centroid,Known,Assigned Taxonomy,Internal Taxonomy,Minimum pair-wise ANI,Maximum pair-wise ANI" />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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243 <action name="column_types" type="metadata" default="str,str,float,int,int,str,str,str,str,str,str,float,float" />
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244 </actions>
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245 </data>
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246
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247 <!-- Table with list of genomes and their assignments -->
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248 <data format="tabular" name="genomes_table" label="${tool.name} on ${on_string}: genomes" from_work_dir="genomes.tsv">
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249 <actions>
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250 <action name="column_names" type="metadata" default="Genome,Type,Assigned Taxonomy,Internal Taxonomy" />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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251 <action name="column_types" type="metadata" default="str,str,str,str" />
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252 </actions>
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253 </data>
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254
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255 <!-- Database as compressed tarball -->
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256 <data format="tar" name="database" label="${tool.name} on ${on_string}: database" from_work_dir="MetaSBT-Database.tar.gz" />
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257 </outputs>
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258
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259 <tests>
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260 <test expect_num_outputs="3">
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261 <param name="genomes" value="genome_1.fna.gz,genome_2.fna.gz,genome_3.fna.gz,genome_4.fna.gz,genome_5.fna.gz,genome_6.fna.gz" ftype="fasta.gz" />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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262
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263 <param name="advanced|index_update_conditional|index_update_option" value="true" />
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264 <param name="advanced|index_update_conditional|database_selection|source" value="history" />
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265 <param name="advanced|index_update_conditional|database_selection|db_tarball" ftype="tar" value="MetaSBT-Test-20250620.1.tar.gz" />
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266
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267 <output name="clusters_table" ftype="tabular">
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268 <assert_contents>
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269 <has_text text="k__Viruses|p__Nucleocytoviricota|c__Pokkesviricetes|o__Chitovirales|f__Poxviridae|g__Orthopoxvirus|s__Monkeypox_virus" />
47189346d00d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt commit 5509a3fab8eb49e931a5fde335dd7030e16737f5
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270 </assert_contents>
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271 </output>
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272
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273 <output name="genomes_table" ftype="tabular">
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274 <assert_contents>
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275 <has_text text="genome_1" />
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276 <has_text text="genome_2" />
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277 <has_text text="genome_3" />
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278 <has_text text="genome_4" />
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279 </assert_contents>
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280 </output>
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281
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282 <output name="database" ftype="tar">
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283 <assert_contents>
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284 <has_size value="468556" delta="10000"/>
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285 </assert_contents>
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286 </output>
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287 </test>
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288
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289 <test expect_num_outputs="3">
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290 <param name="genomes" value="genome_1.fna.gz,genome_2.fna.gz,genome_3.fna.gz,genome_4.fna.gz,genome_5.fna.gz,genome_6.fna.gz" ftype="fasta.gz" />
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291
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292 <param name="advanced|index_update_conditional|index_update_option" value="true" />
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293 <param name="advanced|index_update_conditional|database_selection|source" value="cvmfs" />
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294 <param name="advanced|index_update_conditional|database_selection|db_tarball" value="test_db" />
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295
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296 <output name="clusters_table" ftype="tabular">
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297 <assert_contents>
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298 <has_text text="k__Viruses|p__Nucleocytoviricota|c__Pokkesviricetes|o__Chitovirales|f__Poxviridae|g__Orthopoxvirus|s__Monkeypox_virus" />
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299 </assert_contents>
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300 </output>
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301
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302 <output name="genomes_table" ftype="tabular">
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303 <assert_contents>
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304 <has_text text="genome_1" />
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305 <has_text text="genome_2" />
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306 <has_text text="genome_3" />
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307 <has_text text="genome_4" />
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308 </assert_contents>
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309 </output>
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310
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311 <output name="database" ftype="tar">
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312 <assert_contents>
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313 <has_size value="468556" delta="10000"/>
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314 </assert_contents>
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315 </output>
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316 </test>
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317 </tests>
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318
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319 <help>
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320 <![CDATA[
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321 **What it does**
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322
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323 MetaSBT is a scalable framework for the characterization of known and still unknown microbial genomes with Sequence Bloom Trees.
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324 This tool act as an interface to the `index` and `update` subroutines of MetaSBT for the generation and update of new or predefined public databases.
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325
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326 -----
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327
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328 .. class:: infomark
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329
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330 Please visit the official GitHub repository_ for additional information about MetaSBT.
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331 Public MetaSBT Databases are available at the official MetaSBT-DBs_ repository.
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332
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333 .. _repository: https://github.com/cumbof/MetaSBT
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334 .. _MetaSBT-DBs: https://github.com/cumbof/MetaSBT-DBs
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335 ]]>
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336 </help>
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337
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338 <expand macro="citations"/>
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339 </tool>