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comparison prokka.xml @ 18:d643e3b03500 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"
author iuc
date Sat, 13 Feb 2021 11:58:58 +0000
parents 111884f0d912
children 8a22554cdde2
comparison
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17:111884f0d912 18:d643e3b03500
1 <tool id="prokka" name="Prokka" version="1.14.5+galaxy0"> 1 <tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Prokaryotic genome annotation</description> 2 <description>Prokaryotic genome annotation</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.14.6</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.14.5">prokka</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">prokka</requirement>
5 </requirements> 9 </requirements>
6 10
7 <version_command>prokka --version</version_command> 11 <version_command>prokka --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
9 prokka 13 prokka
72 #end if 76 #end if
73 $input 77 $input
74 ]]></command> 78 ]]></command>
75 <inputs> 79 <inputs>
76 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> 80 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
77 <param name="locustag" type="text" value="" label="Locus tag prefix (--locustag)" /> 81 <param argument="--locustag" type="text" value="" label="Locus tag prefix" />
78 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" /> 82 <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" />
79 <param name="gffver" type="select" label="GFF version (--gffver)"> 83 <param argument="--gffver" type="select" label="GFF version">
80 <option value="3">3</option> 84 <option value="3">3</option>
81 <option value="2">2</option> 85 <option value="2">2</option>
82 <option value="1">1</option> 86 <option value="1">1</option>
83 </param> 87 </param>
84 <conditional name="compliant"> 88 <conditional name="compliant">
85 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)"> 89 <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance"
90 help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)">
86 <option value="no">No</option> 91 <option value="no">No</option>
87 <option value="yes">Yes</option> 92 <option value="yes">Yes</option>
88 </param> 93 </param>
89 <when value="no"> 94 <when value="no">
90 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" /> 95 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
91 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" /> 96 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
92 </when> 97 </when>
93 <when value="yes" /> 98 <when value="yes" />
94 </conditional> 99 </conditional>
95 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" /> 100 <param argument="--centre" type="text" value="" label="Sequencing centre ID" />
96 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" /> 101 <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" />
97 <param name="species" type="text" value="" label="Species name (--species)" /> 102 <param argument="--species" type="text" value="" label="Species name" />
98 <param name="strain" type="text" value="" label="Strain name (--strain)" /> 103 <param argument="--strain" type="text" value="" label="Strain name" />
99 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" /> 104 <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" />
100 <conditional name="kingdom"> 105 <conditional name="kingdom">
101 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)"> 106 <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)">
102 <option value="Archaea">Archaea</option> 107 <option value="Archaea">Archaea</option>
103 <option value="Bacteria" selected="true">Bacteria</option> 108 <option value="Bacteria" selected="true">Bacteria</option>
104 <option value="Viruses">Viruses</option> 109 <option value="Viruses">Viruses</option>
105 </param> 110 </param>
106 <when value="Archaea"> 111 <when value="Archaea">
107 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> 112 <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
108 </when> 113 </when>
109 <when value="Bacteria"> 114 <when value="Bacteria">
110 <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> 115 <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
111 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)"> 116 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
112 <option selected="true" value="none">N/A</option> 117 <option selected="true" value="none">N/A</option>
113 <option value="pos">positive</option> 118 <option value="pos">positive</option>
114 <option value="neg">negative</option> 119 <option value="neg">negative</option>
115 </param> SignalP is not FOSS --> 120 </param> SignalP is not FOSS -->
116 </when> 121 </when>
117 <when value="Viruses"> 122 <when value="Viruses">
118 <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> 123 <param argument="--gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
119 </when> 124 </when>
120 </conditional> 125 </conditional>
121 <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" /> 126 <param argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" />
122 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" /> 127 <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" />
123 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" /> 128 <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" />
124 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" /> 129 <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" />
125 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" /> 130 <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
126 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" /> 131 <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
127 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> 132 <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
128 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> 133 <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
129 134
130 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs"> 135 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
131 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option> 136 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
132 <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence (.gbk)</option> 137 <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence (.gbk)</option>
133 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option> 138 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>