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comparison prokka.xml @ 8:392255fa7ab9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
author iuc
date Fri, 28 Oct 2016 13:03:19 -0400
parents f5e44aad6498
children fd4b2f03cfc6
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7:f5e44aad6498 8:392255fa7ab9
1 <tool id="prokka" name="Prokka" version="1.11.0"> 1 <tool id="prokka" name="Prokka" version="1.11.1">
2 <description>prokaryotic genome annotation</description> 2 <description>prokaryotic genome annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.31">blast+</requirement> 4 <requirement type="package" version="1.11">prokka</requirement>
5 <requirement type="package" version="3.1b2">hmmer</requirement> 5 </requirements>
6 <requirement type="package" version="1.2.36">aragorn</requirement> 6 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
7 <requirement type="package" version="2.60">prodigal</requirement> 7 <stdio>
8 <requirement type="package" version="24.3">tbl2asn</requirement> 8 <exit_code range="1:" />
9 <requirement type="package" version="20131122">gnu_parallel</requirement> 9 </stdio>
10 <requirement type="package" version="0.7">barrnap</requirement> 10 <version_command>prokka --version</version_command>
11 <requirement type="package" version="1.1">infernal</requirement> 11 <command><![CDATA[
12 <requirement type="package" version="0.1.6">minced</requirement> 12 prokka
13 <requirement type="package" version="1.11">prokka</requirement> 13 --cpus \${GALAXY_SLOTS:-8}
14 </requirements> 14 --quiet ## to avoid non-error messages written to stderr
15 <version_command>prokka --version</version_command> 15 --outdir outdir --prefix prokka ## used in outputs section
16 <command> 16 #if $locustag
17 prokka 17 --locustag '$locustag'
18 --cpus \${GALAXY_SLOTS:-8} 18 #end if
19 --quiet ## to avoid non-error messages written to stderr 19 #if str($increment)
20 --outdir outdir --prefix prokka ## used in outputs section 20 --increment $increment
21 #if $locustag 21 #end if
22 --locustag "$locustag" 22 --gffver $gffver
23 #if $compliant.compliant_select == "no"
24 #if $compliant.addgenes
25 --addgenes
23 #end if 26 #end if
24 #if str($increment) 27 #if str($compliant.mincontig)
25 --increment $increment 28 --mincontig $compliant.mincontig
26 #end if 29 #end if
27 --gffver $gffver 30 #else
28 #if $compliant.compliant_select == "no" 31 --compliant
29 #if $compliant.addgenes 32 #end if
30 --addgenes 33 #if $centre
31 #end if 34 --centre '$centre'
32 #if str($compliant.mincontig) 35 #end if
33 --mincontig $compliant.mincontig 36 #if $genus
34 #end if 37 --genus '$genus'
35 #else 38 #end if
36 --compliant 39 #if $species
37 #end if 40 --species '$species'
38 #if $centre 41 #end if
39 --centre "$centre" 42 #if $strain
40 #end if 43 --strain '$strain'
41 #if $genus 44 #end if
42 --genus "$genus" 45 #if $plasmid
43 #end if 46 --plasmid '$plasmid'
44 #if $species 47 #end if
45 --species "$species" 48 --kingdom $kingdom.kingdom_select
46 #end if 49 #if str($kingdom.gcode)
47 #if $strain 50 --gcode $kingdom.gcode
48 --strain "$strain" 51 #end if
49 #end if 52 #if $usegenus
50 #if $plasmid 53 --usegenus
51 --plasmid "$plasmid" 54 #end if
52 #end if 55 #if $proteins
53 --kingdom $kingdom.kingdom_select 56 --proteins '$proteins'
54 #if str($kingdom.gcode) 57 #end if
55 --gcode $kingdom.gcode 58 #if $metagenome
56 #end if 59 --metagenome
57 #if $usegenus 60 #end if
58 --usegenus 61 #if $fast
59 #end if 62 --fast
60 #if $proteins 63 #end if
61 --proteins $proteins 64 #if str($evalue)
62 #end if 65 --evalue $evalue
63 #if $metagenome 66 #end if
64 --metagenome 67 #if $rfam
65 #end if 68 --rfam
66 #if $fast 69 #end if
67 --fast 70 #if $norrna
68 #end if 71 --norrna
69 #if str($evalue) 72 #end if
70 --evalue $evalue 73 #if $notrna
71 #end if 74 --notrna
72 #if $rfam 75 #end if
73 --rfam 76 $input
74 #end if 77 ]]></command>
75 #if $norrna 78 <inputs>
76 --norrna 79 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
77 #end if 80 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
78 #if $notrna 81 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
79 --notrna 82 <param name="gffver" type="select" label="GFF version (--gffver)">
80 #end if 83 <option value="3">3</option>
81 $input 84 <option value="2">2</option>
82 </command> 85 <option value="1">1</option>
83 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> 86 </param>
84 <stdio> 87 <conditional name="compliant">
85 <exit_code range="1:" /> 88 <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)">
86 </stdio> 89 <option value="no">No</option>
87 <inputs> 90 <option value="yes">Yes</option>
88 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> 91 </param>
89 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" /> 92 <when value="no">
90 <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)"> 93 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
91 <validator type="in_range" min="1" /> 94 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
92 </param> 95 </when>
93 <param name="gffver" type="select" label="GFF version (--gffver)"> 96 <when value="yes" />
94 <option value="3">3</option> 97 </conditional>
95 <option value="2">2</option> 98 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
96 <option value="1">1</option> 99 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
97 </param> 100 <param name="species" type="text" value="" label="Species name (--species)" />
98 <conditional name="compliant"> 101 <param name="strain" type="text" value="" label="Strain name (--strain)" />
99 <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)"> 102 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
100 <option value="no">No</option> 103 <conditional name="kingdom">
101 <option value="yes">Yes</option> 104 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
102 </param> 105 <option value="Archaea">Archaea</option>
103 <when value="no"> 106 <option value="Bacteria" selected="true">Bacteria</option>
104 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" /> 107 <option value="Viruses">Viruses</option>
105 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" /> 108 </param>
106 </when> 109 <when value="Archaea">
107 <when value="yes" /> 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 -->
108 </conditional> 111 </when>
109 <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" /> 112 <when value="Bacteria">
110 <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" /> 113 <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 -->
111 <param name="species" type="text" value="" label="Species name (--species)" /> 114 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
112 <param name="strain" type="text" value="" label="Strain name (--strain)" /> 115 <option selected="true" value="none">N/A</option>
113 <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" /> 116 <option value="pos">positive</option>
114 <conditional name="kingdom"> 117 <option value="neg">negative</option>
115 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)"> 118 </param> SignalP is not FOSS -->
116 <option value="Archaea">Archaea</option> 119 </when>
117 <option value="Bacteria" selected="true">Bacteria</option> 120 <when value="Viruses">
118 <option value="Viruses">Viruses</option> 121 <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 -->
119 </param> 122 </when>
120 <when value="Archaea"> 123 </conditional>
121 <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 --> 124 <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" />
122 </when> 125 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
123 <when value="Bacteria"> 126 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
124 <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 --> 127 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
125 <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)"> 128 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
126 <option selected="true" value="none">N/A</option> 129 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
127 <option value="pos">positive</option> 130 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
128 <option value="neg">negative</option> 131 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
129 </param> SignalP is not FOSS --> 132
130 </when> 133 <param name="outputs" type="select" multiple="true" label="Additional outputs">
131 <when value="Viruses"> 134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option>
132 <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 --> 135 <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</option>
133 </when> 136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option>
134 </conditional> 137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option>
135 <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" /> 138 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</option>
136 <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" /> 139 <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.</option>
137 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" /> 140 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option>
138 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" /> 141 <option value="tbl" selected="True">Feature Table file</option>
139 <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off"> 142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option>
140 <validator type="in_range" min="0" /> 143 <option value="txt" selected="True">Statistics relating to the annotated features found</option>
141 </param> 144 </param>
142 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" /> 145
143 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> 146 </inputs>
144 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> 147 <outputs>
145 </inputs> 148 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
146 <outputs> 149 <filter>'gff' in outputs</filter>
147 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff" /> 150 </data>
148 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk" /> 151 <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
149 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna" /> 152 <filter>'gbk' in outputs</filter>
150 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa" /> 153 </data>
151 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn" /> 154 <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
152 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn" /> 155 <filter>'fna' in outputs</filter>
153 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa" /> 156 </data>
154 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl" /> 157 <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
155 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err" /> 158 <filter>'faa' in outputs</filter>
156 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt" /> 159 </data>
157 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" /> 160 <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
158 </outputs> 161 <filter>'ffn' in outputs</filter>
159 <help> 162 </data>
163 <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
164 <filter>'sqn' in outputs</filter>
165 </data>
166 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
167 <filter>'fsa' in outputs</filter>
168 </data>
169 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
170 <filter>'tbl' in outputs</filter>
171 </data>
172 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
173 <filter>'err' in outputs</filter>
174 </data>
175 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
176 <filter>'txt' in outputs</filter>
177 </data>
178 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
179 </outputs>
180 <tests>
181 <test>
182 <param name="input" ftype="fasta" value="phiX174.fasta" />
183 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" />
184 <output name="out_gff" file="out.gff" />
185 <output name="out_gbk" file="out.gbk" lines_diff="14" />
186 <output name="out_fna" file="out.fna" />
187 <output name="out_faa" file="out.faa" />
188 <output name="out_ffn" file="out.ffn" />
189 <output name="out_sqn" file="out.sqn" lines_diff="84" />
190 <output name="out_fsa" file="out.fsa" />
191 <output name="out_tbl" file="out.tbl" />
192 <output name="out.err" file="out.err" />
193 <output name="out_txt" file="out.txt" />
194 <output name="out_log">
195 <assert_contents>
196 <has_text text="Type 'prokka --citation' for more details." />
197 </assert_contents>
198 </output>
199 </test>
200 </tests>
201 <help><![CDATA[
160 **What it does** 202 **What it does**
161 203
162 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ. 204 Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
163 205
164 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
190 txt 232 txt
191 Statistics relating to the annotated features found 233 Statistics relating to the annotated features found
192 234
193 **License and citation** 235 **License and citation**
194 236
195 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_. 237 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
196 238
197 .. _CRS4 Srl.: http://www.crs4.it/ 239 .. _CRS4 Srl.: http://www.crs4.it/
198 .. _MIT license: http://opensource.org/licenses/MIT 240 .. _Earlham Institute: http://earlham.ac.uk/
241 .. _MIT license: https://opensource.org/licenses/MIT
199 242
200 You can use this tool only if you agree to the license terms of: `Prokka`_. 243 You can use this tool only if you agree to the license terms of: `Prokka`_.
201 244
202 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 245 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
203 </help> 246 ]]></help>
204 <citations> 247 <citations>
205 <citation type="doi">10.1093/bioinformatics/btu135</citation> 248 <citation type="doi">10.1093/bioinformatics/btu135</citation>
206 <citation type="doi">10.1093/bioinformatics/btu153</citation> 249 <citation type="doi">10.1093/bioinformatics/btu153</citation>
207 </citations> 250 </citations>
208 </tool> 251 </tool>