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comparison panaroo.xml @ 2:b05be6316263 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo commit 95eb601ee5e08ebcca551bd949b83e0b85718df8
author iuc
date Tue, 20 Jan 2026 13:23:28 +0000
parents b6a78d286482
children
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1:b6a78d286482 2:b05be6316263
26 $advanced.remove_invalid_genes 26 $advanced.remove_invalid_genes
27 #end if 27 #end if
28 --threshold '$advanced.matching_option.threshold' 28 --threshold '$advanced.matching_option.threshold'
29 --family_threshold '$advanced.matching_option.family_threshold' 29 --family_threshold '$advanced.matching_option.family_threshold'
30 --len_dif_percent '$advanced.matching_option.len_dif_percent' 30 --len_dif_percent '$advanced.matching_option.len_dif_percent'
31 --family_len_dif_percent '$advanced.matching_option.family_len_dif_percent'
31 $advanced.matching_option.merge_paralogs 32 $advanced.matching_option.merge_paralogs
32 --search_radius '$advanced.refind_option.search_radius' 33 --search_radius '$advanced.refind_option.search_radius'
33 --refind_prop_match '$advanced.refind_option.refind_prop_match' 34 --refind_prop_match '$advanced.refind_option.refind_prop_match'
34 --refind-mode '$advanced.refind_option.refind_mode' 35 --refind-mode '$advanced.refind_option.refind_mode'
35 --min_trailing_support '$advanced.graph_correction_option.min_trailing_support' 36 --min_trailing_support '$advanced.graph_correction_option.min_trailing_support'
82 <!--Options for Matching--> 83 <!--Options for Matching-->
83 <section name="matching_option" title="Matching" expanded="false"> 84 <section name="matching_option" title="Matching" expanded="false">
84 <param argument="--threshold" type="float" value="0.98" label="Sequence identity threshold" help="default: 0.98"/> 85 <param argument="--threshold" type="float" value="0.98" label="Sequence identity threshold" help="default: 0.98"/>
85 <param argument="--family_threshold" type="float" value="0.7" label="Protein family sequence identity threshold" help="default: 0.7"/> 86 <param argument="--family_threshold" type="float" value="0.7" label="Protein family sequence identity threshold" help="default: 0.7"/>
86 <param argument="--len_dif_percent" type="float" value="0.98" label="Length difference cutoff" help="default: 0.98"/> 87 <param argument="--len_dif_percent" type="float" value="0.98" label="Length difference cutoff" help="default: 0.98"/>
88 <param argument="--family_len_dif_percent" type="float" value="0.0" label="Length difference cutoff at the gene family level" help="default: 0.0"/>
87 <param argument="--merge-paralogs" type="boolean" truevalue="--merge_paralogs" falsevalue="" label="Merge Paralogs"/> 89 <param argument="--merge-paralogs" type="boolean" truevalue="--merge_paralogs" falsevalue="" label="Merge Paralogs"/>
88 </section> 90 </section>
89 91
90 <!--Options for Refind--> 92 <!--Options for Refind-->
91 <section name="refind_option" title="Refind" expanded="false"> 93 <section name="refind_option" title="Refind" expanded="false">