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comparison lexicmap.xml @ 5:f0e5afff062b 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 09:42:53 +0000
parents feedc23590ad
children
comparison
equal deleted inserted replaced
4:feedc23590ad 5:f0e5afff062b
11 #set INDICES = [db.extra_files_path for db in $db_opts.histdb] 11 #set INDICES = [db.extra_files_path for db in $db_opts.histdb]
12 #else: 12 #else:
13 #set INDICES = $db_opts.lexicmap_index.fields.path.split(",") 13 #set INDICES = $db_opts.lexicmap_index.fields.path.split(",")
14 #end if 14 #end if
15 15
16 extract_query_ids() {
17 local input_files="\$1";
18 local query_ids="";
19 IFS=',' read -ra files <<< "\$input_files";
20 query_ids="";
21 for query_file in "\${files[@]}"; do
22 if file --mime-type "\$query_file" | grep -q "gzip"; then
23 query_ids+=\$(zcat "\$query_file" | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
24 else
25 query_ids+=\$(cat "\$query_file" | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
26 fi
27 done;
28 declare -g -a query_array=();
29 IFS='>' read -r -a query_array <<< "\$query_ids";
30 }
31 &&
32 #for $counter, $index in enumerate($INDICES): 16 #for $counter, $index in enumerate($INDICES):
17 set -eu;
33 lexicmap search 18 lexicmap search
34
35 --threads "\${GALAXY_SLOTS:-1}" 19 --threads "\${GALAXY_SLOTS:-1}"
36
37 ${load_whole_seeds} 20 ${load_whole_seeds}
38 ${all} 21 ${all}
39 22
40 --index '${index}' 23 --index '${index}'
41 24
68 #end if 51 #end if
69 && 52 &&
70 #end for 53 #end for
71 54
72 #if len($INDICES) > 1 55 #if len($INDICES) > 1
56 query_ids="";
57 #for $query_file in $query
58 #if $query_file.is_of_type("fasta.gz")
59 query_ids+=\$(zcat '$query_file' | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
60 #else
61 query_ids+=\$(cat '$query_file' | grep '^>' | while IFS= read -r line; do clean="\${line#>}"; echo "\${clean%% *}>"; done);
62 #end if
63 #end for
64 IFS='>' read -r -a query_array <<< "\$query_ids";
73 counter=0 && 65 counter=0 &&
74 extract_query_ids '$query' &&
75 for ((i=0; i<\${#query_array[@]}; i++)); do 66 for ((i=0; i<\${#query_array[@]}; i++)); do
76 counter=\$((counter + 1)); 67 counter=\$((counter + 1));
77 lexicmap utils merge-search-results 68 lexicmap utils merge-search-results
78 --out-file "combined_result.\${counter}.tsv" 69 --out-file "combined_result.\${counter}.tsv"
79 -q "\${query_array[\$i]}" lexicmap_search_result__index*.tsv 70 -q "\${query_array[\$i]}" lexicmap_search_result__index*.tsv
83 #else 74 #else
84 mv lexicmap_search_result__index0.tsv '$out_file' 75 mv lexicmap_search_result__index0.tsv '$out_file'
85 #end if 76 #end if
86 ]]></command> 77 ]]></command>
87 <inputs> 78 <inputs>
88 <param name="query" type="data" format="fasta.gz" label="LexicMap query file" multiple="true" help=""/> 79 <param name="query" type="data" format="@FASTA_TYPES@" label="LexicMap query file" multiple="true" help=""/>
89 <conditional name="db_opts"> 80 <conditional name="db_opts">
90 <param name="db_opts_selector" type="select" label="LexiMap index source"> 81 <param name="db_opts_selector" type="select" label="LexiMap index source">
91 <option value="histdb">From your history</option> 82 <option value="histdb">From your history</option>
92 <option value="db" selected="true">Locally installed LexicMap indexes</option> 83 <option value="db" selected="true">Locally installed LexicMap indexes</option>
93 </param> 84 </param>