Mercurial > repos > iuc > lexicmap

annotate lexicmap.xml @ 2:73accf8f68a9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
author iuc
date Thu, 18 Sep 2025 11:27:35 +0000
parents 2e6641136004
children 73480ee77517
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
3 <macros>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
4 <import>macros.xml</import>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
5 </macros>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
6 <expand macro="bio_tools"/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
8
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
10
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
11 lexicmap search
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
12
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
13 --threads "\${GALAXY_SLOTS:-1}"
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
14
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
15 ${load_whole_seeds}
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
16 ${all}
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
17
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
18 #if $db_opts.db_opts_selector == "histdb"
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
19 --index '${db_opts.histdb.extra_files_path}'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
20 #else:
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
22 #end if
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
23
2
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
24 #for $q in $query
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
25 '$q'
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
26 #end for
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
27
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
28 --out-file '$out_file'
0
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
29
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
30 --top-n-genomes '$top_n_genomes'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
31
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
32 --align-band '$align_band'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
33 --align-ext-len '$align_ext_len'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
34 --align-max-gap '$align_max_gap'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
35 --align-min-match-len '$align_min_match_len'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
36 --align-min-match-pident '$align_min_match_pident'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
37 --max-evalue '$max_evalue'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
38 --max-query-conc '$max_query_conc'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
39 --seed-max-dist '$seed_max_dist'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
40 --seed-max-gap '$seed_max_gap'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
41 --seed-min-prefix '$seed_min_prefix'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
42 --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
iuc
parents:
diff changeset
43
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
44 #if $min_qcov_per_genome
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
45 --min-qcov-per-genome '$min_qcov_per_genome'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
46 #end if
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
47
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
48 #if $min_qcov_per_hsp
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
49 --min-qcov-per-hsp '$min_qcov_per_hsp'
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
50 #end if
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
51
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
52 ]]></command>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
53 <inputs>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
54 <param name="query" type="data" format="fasta.gz" label="LexicMap query file" multiple="true" help=""/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
55 <conditional name="db_opts">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
56 <param name="db_opts_selector" type="select" label="LexiMap index source">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
57 <option value="histdb" selected="true">From your history</option>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
58 <option value="db">Locally installed LexicMap indexes</option>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
59 </param>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
60 <when value="histdb">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
61 <param name="histdb" type="data" format="lexicmap_index" optional="false" label="LexicMap index" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
62 </when>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
63 <when value="db">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
64 <param name="lexicmap_index" type="select" optional="false" label="LexicMap index file">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
65 <options from_data_table="lexicmap_index"/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
66 </param>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
67 </when>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
68 </conditional>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
69 <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
iuc
parents:
diff changeset
70 <section name="advanced_settings" title="Advanced settings" expanded="false">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
71 <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
iuc
parents:
diff changeset
72 <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
iuc
parents:
diff changeset
73 <param argument="-align-max-gap" value="20" type="integer" label="Align max gap" help="Maximum gap in a HSP segment." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
74 <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
iuc
parents:
diff changeset
75 <param argument="--align-min-match-pident" value="70" type="float" label="Align min match pident" help="Minimum base identity (percentage) in a HSP segment." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
76 <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
iuc
parents:
diff changeset
77 <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" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
78 <param argument="--max-evalue" value="10" type="float" label="Max evalue" help="Maximum evalue of a HSP segment." />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
79 <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
iuc
parents:
diff changeset
80 <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
iuc
parents:
diff changeset
81 <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
iuc
parents:
diff changeset
82 <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
iuc
parents:
diff changeset
83 <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
iuc
parents:
diff changeset
84 <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
iuc
parents:
diff changeset
85 <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
iuc
parents:
diff changeset
86 </section>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
87 </inputs>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
88 <outputs>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
89 <data name="out_file" format="tabular">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
90 <actions>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
91 <conditional name="advanced_settings.all">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
92 <when value="true">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
93 <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" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
94 </when>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
95 <when value="false">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
96 <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" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
97 </when>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
98 </conditional>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
99 </actions>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
100 </data>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
101 </outputs>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
102 <tests>
2
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
103 <!-- Test 1 - query a local index with one query -->
0
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
104 <test expect_num_outputs="1">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
105 <conditional name="db_opts">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
106 <param name="db_opts_selector" value="db"/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
107 <param name="lexicmap_index" value="LexicMapIndex1" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
108 </conditional>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
109 <param name="query" value="lexicmap_query.fasta.gz" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
110 <section name="advanced_settings">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
111 <param name="load_whole_seeds" value="true" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
112 </section>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
113 <output name="out_file" value="lexicmap_query_result.tsv" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
114 </test>
2
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
115 <!-- Test 2 - query a local index with multiple query files -->
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
116 <test expect_num_outputs="1">
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
117 <conditional name="db_opts">
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
118 <param name="db_opts_selector" value="db"/>
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
119 <param name="lexicmap_index" value="LexicMapIndex1" />
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
120 </conditional>
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
121 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz" />
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
122 <section name="advanced_settings">
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
123 <param name="load_whole_seeds" value="true" />
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
124 </section>
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
125 <output name="out_file" value="lexicmap_query_result2.tsv" />
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
126 </test>
73accf8f68a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit 27bb723932bd00a1cca05557712c473f0088bbfb
iuc
parents: 0
diff changeset
127 <!-- Test 3 - query a index found in the history with one query -->
0
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
128 <test expect_num_outputs="1">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
129 <conditional name="db_opts">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
130 <param name="db_opts_selector" value="histdb"/>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
131 <param name="histdb" ftype="lexicmap_index" class="Directory" value="db.lmi" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
132 </conditional>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
133 <param name="top_n_genomes" value="0" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
134 <param name="query" value="lexicmap_query.fasta.gz" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
135 <section name="advanced_settings">
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
136 <param name="load_whole_seeds" value="true" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
137 </section>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
138 <output name="out_file" value="lexicmap_query_result.tsv" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
139 </test>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
140 </tests>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
141 <help><![CDATA[
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
142
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
143 Search sequences against an LexicMap index Database. For more information about settings
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
144 please visit: https://bioinf.shenwei.me/LexicMap/usage/search
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
145
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
146 Output format:
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
147 Tab-delimited format with 20+ columns, with 1-based positions.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
148
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
149 1. query, Query sequence ID.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
150 2. qlen, Query sequence length.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
151 3. hits, Number of subject genomes.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
152 4. sgenome, Subject genome ID.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
153 5. sseqid, Subject sequence ID.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
154 6. qcovGnm, Query coverage (percentage) per genome: $(aligned bases in the genome)/$qlen.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
155 7. cls, Nth HSP cluster in the genome. (just for improving readability)
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
156 It's useful to show if multiple adjacent HSPs are collinear.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
157 8. hsp, Nth HSP in the genome. (just for improving readability)
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
158 9. qcovHSP Query coverage (percentage) per HSP: $(aligned bases in a HSP)/$qlen.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
159 10. alenHSP, Aligned length in the current HSP.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
160 11. pident, Percentage of identical matches in the current HSP.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
161 12. gaps, Gaps in the current HSP.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
162 13. qstart, Start of alignment in query sequence.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
163 14. qend, End of alignment in query sequence.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
164 15. sstart, Start of alignment in subject sequence.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
165 16. send, End of alignment in subject sequence.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
166 17. sstr, Subject strand.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
167 18. slen, Subject sequence length.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
168 19. evalue, Expect value.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
169 20. bitscore, Bit score.
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
170 21. cigar, CIGAR string of the alignment. (optional with --all)
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
171 22. qseq, Aligned part of query sequence. (optional with --all)
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
172 23. sseq, Aligned part of subject sequence. (optional with --all)
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
173 24. align, Alignment text ("|" and " ") between qseq and sseq. (optional with --all)
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
174
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
175 @info@
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
176 ]]></help>
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
177 <expand macro="citations" />
2e6641136004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
iuc
parents:
diff changeset
178 </tool>