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comparison lexicmap.xml @ 4:0004a511baff draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit eceb4b3a69c5a755feac55801e85eb914a669042
author iuc
date Thu, 20 Nov 2025 19:38:27 +0000
parents 73480ee77517
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3:73480ee77517 4:0004a511baff
86 ]]></command> 86 ]]></command>
87 <inputs> 87 <inputs>
88 <param name="query" type="data" format="fasta.gz" label="LexicMap query file" multiple="true" help=""/> 88 <param name="query" type="data" format="fasta.gz" label="LexicMap query file" multiple="true" help=""/>
89 <conditional name="db_opts"> 89 <conditional name="db_opts">
90 <param name="db_opts_selector" type="select" label="LexiMap index source"> 90 <param name="db_opts_selector" type="select" label="LexiMap index source">
91 <option value="histdb" selected="true">From your history</option> 91 <option value="histdb">From your history</option>
92 <option value="db">Locally installed LexicMap indexes</option> 92 <option value="db" selected="true">Locally installed LexicMap indexes</option>
93 </param> 93 </param>
94 <when value="histdb"> 94 <when value="histdb">
95 <param name="histdb" type="data" format="lexicmap_index" optional="false" multiple="true" label="LexicMap index" /> 95 <param name="histdb" type="data" format="lexicmap_index" optional="false" multiple="true" label="LexicMap index" />
96 </when> 96 </when>
97 <when value="db"> 97 <when value="db">
113 <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." /> 113 <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." />
114 <param argument="--min-qcov-per-genome" type="float" optional="true" help="Minimum query coverage (percentage) per genome." /> 114 <param argument="--min-qcov-per-genome" type="float" optional="true" help="Minimum query coverage (percentage) per genome." />
115 <param argument="--min-qcov-per-hsp" type="float" optional="true" help="Minimum query coverage (percentage) per HSP." /> 115 <param argument="--min-qcov-per-hsp" type="float" optional="true" help="Minimum query coverage (percentage) per HSP." />
116 <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." /> 116 <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." />
117 <param argument="--seed-max-gap" value="1000" type="integer" label="Seed max gap" help="Minimum gap in seed chaining." /> 117 <param argument="--seed-max-gap" value="1000" type="integer" label="Seed max gap" help="Minimum gap in seed chaining." />
118 <param argument="--seed-min-prefix" value="15" type="integer" label="Seed min prefix" help="Minimum (prefix/suffix) length of matched seeds (anchors)." /> 118 <param argument="--seed-min-prefix" value="17" type="integer" label="Seed min prefix" help="Minimum (prefix/suffix) length of matched seeds (anchors)." />
119 <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." /> 119 <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." />
120 </section> 120 </section>
121 </inputs> 121 </inputs>
122 <outputs> 122 <outputs>
123 <data name="out_file" format="tabular"> 123 <data name="out_file" format="tabular">
124 <actions> 124 <actions>