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comparison bakta.xml @ 6:92eee5f31117 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta commit fe9aabe924f278694d20b82169edacdb3e91eb49
author iuc
date Sun, 11 Feb 2024 00:56:12 +0000
parents 728dacaf08a9
children ba6990f72184
comparison
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5:728dacaf08a9 6:92eee5f31117
68 #end if 68 #end if
69 $annotation.compliant 69 $annotation.compliant
70 #if $annotation.proteins 70 #if $annotation.proteins
71 --proteins '$annotation.proteins' 71 --proteins '$annotation.proteins'
72 #end if 72 #end if
73 #if $annotation.regions
74 --regions '$annotation.regions'
75 #end if
73 #*====================================== 76 #*======================================
74 Workflow OPTIONS 77 Workflow OPTIONS
75 skip some step of the bakta analysis 78 skip some step of the bakta analysis
76 ======================================*# 79 ======================================*#
77 80
130 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/> 133 <param name="keep_contig_headers" type="boolean" truevalue="--keep-contig-headers" falsevalue="" label="Keep original contig header (--keep-contig-headers)"/>
131 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/> 134 <param argument="--replicons" type="data" format="tabular,csv" optional="true" label="Replicon information table (tsv/csv)" help=""/>
132 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/> 135 <param argument="--compliant" type="boolean" truevalue="--compliant" falsevalue="" label="Force Genbank/ENA/DDJB compliance"/>
133 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/> 136 <param argument="--proteins" type="data" format="fasta" optional="true" label="Protein fasta file" help="Fasta file of trusted protein sequences for CDS annotation"/>
134 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/> 137 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" label="Metagenome mode" help="Run in metagenome mode. This only affects CDS prediction"/>
138 <param argument="--regions" type="data" format="gff,genbank" optional="true" label="Pre-annotated regions" help="Regions only, no functional annotations."/>
135 </section> 139 </section>
136 <!-- PARAMETER FOR WORKFLOW ANALYSIS --> 140 <!-- PARAMETER FOR WORKFLOW ANALYSIS -->
137 <section name="workflow" title="Workflow option to skip steps"> 141 <section name="workflow" title="Workflow option to skip steps">
138 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip"> 142 <param name="skip_analysis" type="select" display="checkboxes" multiple="true" label="Select steps to skip">
139 <option value="--skip-trna">Skip tRNA detection and annotation</option> 143 <option value="--skip-trna">Skip tRNA detection and annotation</option>