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annotate lexicmap.xml @ 0:2e6641136004 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
author iuc
date Tue, 16 Sep 2025 13:51:46 +0000
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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>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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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[
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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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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11 lexicmap search
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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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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13 --threads "\${GALAXY_SLOTS:-1}"
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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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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15 ${load_whole_seeds}
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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16 ${all}
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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18 #if $db_opts.db_opts_selector == "histdb"
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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19 --index '${db_opts.histdb.extra_files_path}'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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20 #else:
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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21 --index '${db_opts.lexicmap_index.fields.path}'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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22 #end if
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2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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24 '$query' --out-file '$out_file'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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26 --top-n-genomes '$top_n_genomes'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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27
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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28 --align-band '$align_band'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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29 --align-ext-len '$align_ext_len'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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30 --align-max-gap '$align_max_gap'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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31 --align-min-match-len '$align_min_match_len'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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32 --align-min-match-pident '$align_min_match_pident'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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33 --max-evalue '$max_evalue'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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34 --max-query-conc '$max_query_conc'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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35 --seed-max-dist '$seed_max_dist'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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36 --seed-max-gap '$seed_max_gap'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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37 --seed-min-prefix '$seed_min_prefix'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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38 --seed-min-single-prefix '$seed_min_single_prefix'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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39
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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40 #if $min_qcov_per_genome
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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41 --min-qcov-per-genome '$min_qcov_per_genome'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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42 #end if
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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43
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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44 #if $min_qcov_per_hsp
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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45 --min-qcov-per-hsp '$min_qcov_per_hsp'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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46 #end if
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47
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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48 ]]></command>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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49 <inputs>
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50 <param name="query" type="data" format="fasta.gz" label="LexicMap query file" multiple="true" help=""/>
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51 <conditional name="db_opts">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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52 <param name="db_opts_selector" type="select" label="LexiMap index source">
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53 <option value="histdb" selected="true">From your history</option>
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54 <option value="db">Locally installed LexicMap indexes</option>
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55 </param>
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56 <when value="histdb">
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57 <param name="histdb" type="data" format="lexicmap_index" optional="false" label="LexicMap index" />
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58 </when>
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59 <when value="db">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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60 <param name="lexicmap_index" type="select" optional="false" label="LexicMap index file">
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61 <options from_data_table="lexicmap_index"/>
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62 </param>
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63 </when>
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64 </conditional>
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65 <param argument="--top-n-genomes" type="integer" value="0" label="Keep top N genome matches for a query (0 for all)" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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66 <section name="advanced_settings" title="Advanced settings" expanded="false">
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67 <param argument="--align-band" value="100" type="integer" label="Align band" help="Band size in backtracking the score matrix (pseudo alignment" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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68 <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." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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69 <param argument="-align-max-gap" value="20" type="integer" label="Align max gap" help="Maximum gap in a HSP segment." />
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70 <param argument="--align-min-match-len" value="50" type="integer" label="Align min match length" help="Minimum aligned length in a HSP segment." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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71 <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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72 <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'." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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73 <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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74 <param argument="--max-evalue" value="10" type="float" label="Max evalue" help="Maximum evalue of a HSP segment." />
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75 <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." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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76 <param argument="--min-qcov-per-genome" type="float" optional="true" help="Minimum query coverage (percentage) per genome." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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77 <param argument="--min-qcov-per-hsp" type="float" optional="true" help="Minimum query coverage (percentage) per HSP." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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78 <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." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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79 <param argument="--seed-max-gap" value="1000" type="integer" label="Seed max gap" help="Minimum gap in seed chaining." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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80 <param argument="--seed-min-prefix" value="15" type="integer" label="Seed min prefix" help="Minimum (prefix/suffix) length of matched seeds (anchors)." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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81 <param argument="--seed-min-single-prefix" value="17" 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." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
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82 </section>
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83 </inputs>
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84 <outputs>
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85 <data name="out_file" format="tabular">
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86 <actions>
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87 <conditional name="advanced_settings.all">
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88 <when value="true">
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89 <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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90 </when>
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91 <when value="false">
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92 <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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93 </when>
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94 </conditional>
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95 </actions>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <test expect_num_outputs="1">
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100 <conditional name="db_opts">
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101 <param name="db_opts_selector" value="db"/>
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102 <param name="lexicmap_index" value="LexicMapIndex1" />
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103 </conditional>
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104 <param name="query" value="lexicmap_query.fasta.gz" />
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105 <section name="advanced_settings">
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106 <param name="load_whole_seeds" value="true" />
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107 </section>
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108 <output name="out_file" value="lexicmap_query_result.tsv" />
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109 </test>
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110 <test expect_num_outputs="1">
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111 <conditional name="db_opts">
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112 <param name="db_opts_selector" value="histdb"/>
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113 <param name="histdb" ftype="lexicmap_index" class="Directory" value="db.lmi" />
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114 </conditional>
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115 <param name="top_n_genomes" value="0" />
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116 <param name="query" value="lexicmap_query.fasta.gz" />
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117 <section name="advanced_settings">
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118 <param name="load_whole_seeds" value="true" />
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119 </section>
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120 <output name="out_file" value="lexicmap_query_result.tsv" />
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124
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125 Search sequences against an LexicMap index Database. For more information about settings
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126 please visit: https://bioinf.shenwei.me/LexicMap/usage/search
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127
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128 Output format:
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129 Tab-delimited format with 20+ columns, with 1-based positions.
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130
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131 1. query, Query sequence ID.
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132 2. qlen, Query sequence length.
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133 3. hits, Number of subject genomes.
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134 4. sgenome, Subject genome ID.
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135 5. sseqid, Subject sequence ID.
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136 6. qcovGnm, Query coverage (percentage) per genome: $(aligned bases in the genome)/$qlen.
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137 7. cls, Nth HSP cluster in the genome. (just for improving readability)
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138 It's useful to show if multiple adjacent HSPs are collinear.
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139 8. hsp, Nth HSP in the genome. (just for improving readability)
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140 9. qcovHSP Query coverage (percentage) per HSP: $(aligned bases in a HSP)/$qlen.
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141 10. alenHSP, Aligned length in the current HSP.
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142 11. pident, Percentage of identical matches in the current HSP.
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143 12. gaps, Gaps in the current HSP.
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144 13. qstart, Start of alignment in query sequence.
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145 14. qend, End of alignment in query sequence.
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146 15. sstart, Start of alignment in subject sequence.
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147 16. send, End of alignment in subject sequence.
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148 17. sstr, Subject strand.
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149 18. slen, Subject sequence length.
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150 19. evalue, Expect value.
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151 20. bitscore, Bit score.
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152 21. cigar, CIGAR string of the alignment. (optional with --all)
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153 22. qseq, Aligned part of query sequence. (optional with --all)
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154 23. sseq, Aligned part of subject sequence. (optional with --all)
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155 24. align, Alignment text ("|" and " ") between qseq and sseq. (optional with --all)
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156
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157 @info@
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158 ]]></help>
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159 <expand macro="citations" />
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160 </tool>