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annotate lexicmap.xml @ 5:1dc577370a86 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 45c03ff07e2d5bba1d490a67434347ec17eb30f4
author iuc
date Thu, 22 Jan 2026 09:42:30 +0000
parents 0004a511baff
children
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2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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1 <tool id="lexicmap_search" name="LexicMap Search" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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2 <description>nucleotide sequence tool for querying genomes</description>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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3 <macros>
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4 <import>macros.xml</import>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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5 </macros>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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6 <expand macro="bio_tools"/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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7 <expand macro="requirements"/>
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2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $db_opts.db_opts_selector == "histdb"
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11 #set INDICES = [db.extra_files_path for db in $db_opts.histdb]
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12 #else:
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13 #set INDICES = $db_opts.lexicmap_index.fields.path.split(",")
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14 #end if
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16 #for $counter, $index in enumerate($INDICES):
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17 set -eu;
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18 lexicmap search
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19 --threads "\${GALAXY_SLOTS:-1}"
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20 ${load_whole_seeds}
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21 ${all}
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23 --index '${index}'
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25 #for $q in $query
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26 '$q'
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27 #end for
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29 --out-file 'lexicmap_search_result__index${counter}.tsv'
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30
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31 --top-n-genomes '$top_n_genomes'
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33 --align-band '$align_band'
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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34 --align-ext-len '$align_ext_len'
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35 --align-max-gap '$align_max_gap'
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36 --align-min-match-len '$align_min_match_len'
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37 --align-min-match-pident '$align_min_match_pident'
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38 --max-evalue '$max_evalue'
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39 --max-query-conc '$max_query_conc'
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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40 --seed-max-dist '$seed_max_dist'
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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41 --seed-max-gap '$seed_max_gap'
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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42 --seed-min-prefix '$seed_min_prefix'
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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43 --seed-min-single-prefix '$seed_min_single_prefix'
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44
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45 #if $min_qcov_per_genome
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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46 --min-qcov-per-genome '$min_qcov_per_genome'
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47 #end if
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48
3
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49 #if $min_qcov_per_hsp
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50 --min-qcov-per-hsp '$min_qcov_per_hsp'
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51 #end if
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52 &&
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53 #end for
0
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54
3
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55 #if len($INDICES) > 1
5
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56 query_ids="";
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57 #for $query_file in $query
1dc577370a86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 45c03ff07e2d5bba1d490a67434347ec17eb30f4
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58 #if $query_file.is_of_type("fasta.gz")
1dc577370a86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 45c03ff07e2d5bba1d490a67434347ec17eb30f4
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59 query_ids+=\$(zcat '$query_file' | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
1dc577370a86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 45c03ff07e2d5bba1d490a67434347ec17eb30f4
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60 #else
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61 query_ids+=\$(cat '$query_file' | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
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62 #end if
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63 #end for
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64 IFS='>' read -r -a query_array <<< "\$query_ids";
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65 counter=0 &&
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66 for ((i=0; i<\${#query_array[@]}; i++)); do
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67 counter=\$((counter + 1));
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68 lexicmap utils merge-search-results
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69 --out-file "combined_result.\${counter}.tsv"
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70 -q "\${query_array[\$i]}" lexicmap_search_result__index*.tsv
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71 -j "\${GALAXY_SLOTS:-1}";
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72 done &&
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73 cat combined_result.*.tsv | awk 'NR==1 || $0 !~ /^query\tqlen\thits/' > '$out_file'
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74 #else
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75 mv lexicmap_search_result__index0.tsv '$out_file'
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76 #end if
0
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77 ]]></command>
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78 <inputs>
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79 <param name="query" type="data" format="@FASTA_TYPES@" label="LexicMap query file" multiple="true" help=""/>
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80 <conditional name="db_opts">
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81 <param name="db_opts_selector" type="select" label="LexiMap index source">
4
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82 <option value="histdb">From your history</option>
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83 <option value="db" selected="true">Locally installed LexicMap indexes</option>
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84 </param>
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85 <when value="histdb">
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86 <param name="histdb" type="data" format="lexicmap_index" optional="false" multiple="true" label="LexicMap index" />
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87 </when>
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88 <when value="db">
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89 <param name="lexicmap_index" type="select" optional="false" multiple="true" label="LexicMap index file">
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90 <options from_data_table="lexicmap_index"/>
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91 </param>
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92 </when>
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93 </conditional>
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94 <param argument="--top-n-genomes" type="integer" value="0" label="Keep top N genome matches for a query (0 for all)" />
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95 <section name="advanced_settings" title="Advanced settings" expanded="false">
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96 <param argument="--align-band" value="100" type="integer" label="Align band" help="Band size in backtracking the score matrix (pseudo alignment" />
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97 <param argument="-align-ext-len" min="0" value="1000" type="integer" label="Align extend length" help="Extend length of upstream and downstream of seed regions, for extracting query and target sequences for alignment. It should be &lt;= contig interval length in database." />
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98 <param argument="-align-max-gap" value="20" type="integer" label="Align max gap" help="Maximum gap in a HSP segment." />
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99 <param argument="--align-min-match-len" value="50" type="integer" label="Align min match length" help="Minimum aligned length in a HSP segment." />
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100 <param argument="--align-min-match-pident" value="70" type="float" label="Align min match pident" help="Minimum base identity (percentage) in a HSP segment." />
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101 <param argument="--all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="All all columns" help="Output more columns, e.g., matched sequences. Use this if you want to output blast-style format with 'lexicmap utils 2blast'." />
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102 <param argument="--load-whole-seeds" type="boolean" truevalue="--load-whole-seeds" falsevalue="" checked="false" label="Load whole seeds" help="Load the whole seed data into memory for faster search" />
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103 <param argument="--max-evalue" value="10" type="float" label="Max evalue" help="Maximum evalue of a HSP segment." />
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104 <param argument="--max-query-conc" value="12" type="integer" label="Max query conc" help="Maximum number of concurrent queries. Bigger values do not improve the batch searching speed and consume much memory." />
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105 <param argument="--min-qcov-per-genome" type="float" optional="true" help="Minimum query coverage (percentage) per genome." />
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106 <param argument="--min-qcov-per-hsp" type="float" optional="true" help="Minimum query coverage (percentage) per HSP." />
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107 <param argument="--seed-max-dist" value="1000" type="integer" label="Seed max dist" help="Minimum distance between seeds in seed chaining. It should be &lt;= contig interval length in database." />
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108 <param argument="--seed-max-gap" value="1000" type="integer" label="Seed max gap" help="Minimum gap in seed chaining." />
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109 <param argument="--seed-min-prefix" value="17" type="integer" label="Seed min prefix" help="Minimum (prefix/suffix) length of matched seeds (anchors)." />
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110 <param argument="--seed-min-single-prefix" value="19" type="integer" label="Seed min single prefix" help="Minimum (prefix/suffix) length of matched seeds (anchors) if there's only one pair of seeds matched." />
0
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111 </section>
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112 </inputs>
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113 <outputs>
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114 <data name="out_file" format="tabular">
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115 <actions>
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116 <conditional name="advanced_settings.all">
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117 <when value="true">
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118 <action name="column_names" type="metadata" default="Qquery,qlen,hits,sgenome,sseqid,qcovGnm,cls,hsp,qcovHSP,alenHSP,pident,gaps,qstart,qend,sstart,send,sstr,slen,evalue,bitscore,cigar,qseq,sseq,align" />
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119 </when>
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120 <when value="false">
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121 <action name="column_names" type="metadata" default="Qquery,qlen,hits,sgenome,sseqid,qcovGnm,cls,hsp,qcovHSP,alenHSP,pident,gaps,qstart,qend,sstart,send,sstr,slen,evalue,bitscore" />
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122 </when>
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123 </conditional>
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124 </actions>
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125 </data>
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126 </outputs>
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127 <tests>
3
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128 <!-- Test 1 - query one local index with one query -->
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129 <test expect_num_outputs="1">
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130 <conditional name="db_opts">
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131 <param name="db_opts_selector" value="db"/>
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132 <param name="lexicmap_index" value="LexicMapIndex1" />
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133 </conditional>
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134 <param name="query" value="lexicmap_query.fasta.gz" />
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135 <section name="advanced_settings">
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136 <param name="load_whole_seeds" value="true" />
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137 </section>
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138 <output name="out_file" value="lexicmap_query_result.tsv" />
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139 </test>
3
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140 <!-- Test 2 - query one local index with multiple query files -->
2
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141 <test expect_num_outputs="1">
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142 <conditional name="db_opts">
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143 <param name="db_opts_selector" value="db"/>
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144 <param name="lexicmap_index" value="LexicMapIndex1" />
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145 </conditional>
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146 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz" />
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147 <section name="advanced_settings">
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148 <param name="load_whole_seeds" value="true" />
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149 </section>
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150 <output name="out_file" value="lexicmap_query_result2.tsv" />
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151 </test>
3
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152 <!-- Test 3 - query two local index with one query file -->
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153 <test expect_num_outputs="1">
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154 <conditional name="db_opts">
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155 <param name="db_opts_selector" value="db"/>
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156 <param name="lexicmap_index" value="LexicMapIndexCombined" />
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157 </conditional>
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158 <param name="query" value="lexicmap_query.fasta.gz" />
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159 <section name="advanced_settings">
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160 <param name="load_whole_seeds" value="true" />
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161 </section>
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162 <output name="out_file" value="lexicmap_query_result.tsv" />
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163 </test>
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164 <!-- Test 4 - query two local index with multiple query files -->
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165 <test expect_num_outputs="1">
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166 <conditional name="db_opts">
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167 <param name="db_opts_selector" value="db"/>
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168 <param name="lexicmap_index" value="LexicMapIndexCombined" />
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169 </conditional>
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170 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz,lexicmap_query3.fasta" />
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171 <section name="advanced_settings">
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172 <param name="load_whole_seeds" value="true" />
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173 </section>
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174 <output name="out_file" value="lexicmap_query_result4.tsv" />
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175 </test>
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176 <!-- Test 5 - query one local index with multiple query files, where only one query will get hits -->
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177 <test expect_num_outputs="1">
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178 <conditional name="db_opts">
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179 <param name="db_opts_selector" value="db"/>
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180 <param name="lexicmap_index" value="LexicMapIndex2" />
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181 </conditional>
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182 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz,lexicmap_query3.fasta" />
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183 <section name="advanced_settings">
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184 <param name="load_whole_seeds" value="true" />
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185 </section>
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186 <output name="out_file" value="lexicmap_query_result3.tsv" />
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187 </test>
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188 <!-- Test 6 - query multiple local index with multiple query files -->
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189 <test expect_num_outputs="1">
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190 <conditional name="db_opts">
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191 <param name="db_opts_selector" value="db"/>
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192 <param name="lexicmap_index" value="LexicMapIndex1,LexicMapIndex2,LexicMapIndexCombined" />
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193 </conditional>
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194
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195 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz,lexicmap_query3.fasta" />
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196 <section name="advanced_settings">
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197 <param name="load_whole_seeds" value="true" />
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198 </section>
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199 <output name="out_file" value="lexicmap_query_result6.tsv" />
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200 </test>
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201 <!-- Test 7 - query one index found in the history with one query -->
0
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202 <test expect_num_outputs="1">
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203 <conditional name="db_opts">
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204 <param name="db_opts_selector" value="histdb"/>
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205 <param name="histdb" ftype="lexicmap_index" class="Directory" value="db.lmi" />
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206 </conditional>
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207 <param name="top_n_genomes" value="0" />
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208 <param name="query" value="lexicmap_query.fasta.gz" />
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209 <section name="advanced_settings">
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210 <param name="load_whole_seeds" value="true" />
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211 </section>
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212 <output name="out_file" value="lexicmap_query_result.tsv" />
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213 </test>
3
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214 <!-- Test 8 - query two index found in the history with one query -->
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215 <test expect_num_outputs="1">
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216 <conditional name="db_opts">
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217 <param name="db_opts_selector" value="histdb"/>
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218 <param name="histdb" ftype="lexicmap_index" class="Directory" value="db.lmi,db2.lmi" />
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219 </conditional>
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220 <param name="top_n_genomes" value="0" />
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221 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query3.fasta" />
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222 <section name="advanced_settings">
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223 <param name="load_whole_seeds" value="true" />
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224 </section>
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225 <output name="out_file" value="lexicmap_query_result5.tsv" />
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226 </test>
0
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227 </tests>
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228 <help><![CDATA[
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229
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230 Search sequences against an LexicMap index Database. For more information about settings
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231 please visit: https://bioinf.shenwei.me/LexicMap/usage/search
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232
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233 Output format:
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234 Tab-delimited format with 20+ columns, with 1-based positions.
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235
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236 1. query, Query sequence ID.
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237 2. qlen, Query sequence length.
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238 3. hits, Number of subject genomes.
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239 4. sgenome, Subject genome ID.
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240 5. sseqid, Subject sequence ID.
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241 6. qcovGnm, Query coverage (percentage) per genome: $(aligned bases in the genome)/$qlen.
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242 7. cls, Nth HSP cluster in the genome. (just for improving readability)
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243 It's useful to show if multiple adjacent HSPs are collinear.
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244 8. hsp, Nth HSP in the genome. (just for improving readability)
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245 9. qcovHSP Query coverage (percentage) per HSP: $(aligned bases in a HSP)/$qlen.
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246 10. alenHSP, Aligned length in the current HSP.
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247 11. pident, Percentage of identical matches in the current HSP.
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248 12. gaps, Gaps in the current HSP.
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249 13. qstart, Start of alignment in query sequence.
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250 14. qend, End of alignment in query sequence.
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251 15. sstart, Start of alignment in subject sequence.
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252 16. send, End of alignment in subject sequence.
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253 17. sstr, Subject strand.
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254 18. slen, Subject sequence length.
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255 19. evalue, Expect value.
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256 20. bitscore, Bit score.
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257 21. cigar, CIGAR string of the alignment. (optional with --all)
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258 22. qseq, Aligned part of query sequence. (optional with --all)
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259 23. sseq, Aligned part of subject sequence. (optional with --all)
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260 24. align, Alignment text ("|" and " ") between qseq and sseq. (optional with --all)
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261
3
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262 When running against multiple indices lexicmap utils merge-search-results will be used to
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263 merge the search results. For more information please visit:
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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264 https://bioinf.shenwei.me/LexicMap/usage/utils/merge-search-results/
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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265
73480ee77517 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit a9227295a4cebc34b17def7b5ca3e4506222b963
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266 Note: if the query id contains spaces, only the first part (before the first space) will be kept as the query id.
0
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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267 @info@
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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268 ]]></help>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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269 <expand macro="citations" />
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270 </tool>