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comparison lexicmap.xml @ 2:73accf8f68a9 draft

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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
comparison
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1:79beb96ffefb 2:73accf8f68a9
19 --index '${db_opts.histdb.extra_files_path}' 19 --index '${db_opts.histdb.extra_files_path}'
20 #else: 20 #else:
21 --index '${db_opts.lexicmap_index.fields.path}' 21 --index '${db_opts.lexicmap_index.fields.path}'
22 #end if 22 #end if
23 23
24 '$query' --out-file '$out_file' 24 #for $q in $query
25 '$q'
26 #end for
27
28 --out-file '$out_file'
25 29
26 --top-n-genomes '$top_n_genomes' 30 --top-n-genomes '$top_n_genomes'
27 31
28 --align-band '$align_band' 32 --align-band '$align_band'
29 --align-ext-len '$align_ext_len' 33 --align-ext-len '$align_ext_len'
94 </conditional> 98 </conditional>
95 </actions> 99 </actions>
96 </data> 100 </data>
97 </outputs> 101 </outputs>
98 <tests> 102 <tests>
103 <!-- Test 1 - query a local index with one query -->
99 <test expect_num_outputs="1"> 104 <test expect_num_outputs="1">
100 <conditional name="db_opts"> 105 <conditional name="db_opts">
101 <param name="db_opts_selector" value="db"/> 106 <param name="db_opts_selector" value="db"/>
102 <param name="lexicmap_index" value="LexicMapIndex1" /> 107 <param name="lexicmap_index" value="LexicMapIndex1" />
103 </conditional> 108 </conditional>
105 <section name="advanced_settings"> 110 <section name="advanced_settings">
106 <param name="load_whole_seeds" value="true" /> 111 <param name="load_whole_seeds" value="true" />
107 </section> 112 </section>
108 <output name="out_file" value="lexicmap_query_result.tsv" /> 113 <output name="out_file" value="lexicmap_query_result.tsv" />
109 </test> 114 </test>
115 <!-- Test 2 - query a local index with multiple query files -->
116 <test expect_num_outputs="1">
117 <conditional name="db_opts">
118 <param name="db_opts_selector" value="db"/>
119 <param name="lexicmap_index" value="LexicMapIndex1" />
120 </conditional>
121 <param name="query" value="lexicmap_query.fasta.gz,lexicmap_query2.fasta.gz" />
122 <section name="advanced_settings">
123 <param name="load_whole_seeds" value="true" />
124 </section>
125 <output name="out_file" value="lexicmap_query_result2.tsv" />
126 </test>
127 <!-- Test 3 - query a index found in the history with one query -->
110 <test expect_num_outputs="1"> 128 <test expect_num_outputs="1">
111 <conditional name="db_opts"> 129 <conditional name="db_opts">
112 <param name="db_opts_selector" value="histdb"/> 130 <param name="db_opts_selector" value="histdb"/>
113 <param name="histdb" ftype="lexicmap_index" class="Directory" value="db.lmi" /> 131 <param name="histdb" ftype="lexicmap_index" class="Directory" value="db.lmi" />
114 </conditional> 132 </conditional>