Mercurial > repos > crs4 > prokka
comparison prokka.xml @ 14:eaee459f3d69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
author | iuc |
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date | Wed, 28 Mar 2018 12:38:42 -0400 |
parents | a17498c603ec |
children | 3a0bd09a41dd |
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13:a17498c603ec | 14:eaee459f3d69 |
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1 <tool id="prokka" name="Prokka" version="1.12.0"> | 1 <tool id="prokka" name="Prokka" version="1.13"> |
2 <description>prokaryotic genome annotation</description> | 2 <description>Prokaryotic genome annotation</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.12">prokka</requirement> | 4 <requirement type="package" version="1.13">prokka</requirement> |
5 </requirements> | 5 </requirements> |
6 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> | 6 |
7 <stdio> | |
8 <exit_code range="1:" /> | |
9 </stdio> | |
10 <version_command>prokka --version</version_command> | 7 <version_command>prokka --version</version_command> |
11 <command><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
12 prokka | 9 prokka |
13 --cpus \${GALAXY_SLOTS:-8} | 10 --cpus \${GALAXY_SLOTS:-8} |
14 --quiet ## to avoid non-error messages written to stderr | 11 --quiet ## to avoid non-error messages written to stderr |
15 --outdir outdir --prefix prokka ## used in outputs section | 12 --outdir outdir --prefix prokka ## used in outputs section |
16 #if $locustag | 13 #if $locustag |
75 #end if | 72 #end if |
76 $input | 73 $input |
77 ]]></command> | 74 ]]></command> |
78 <inputs> | 75 <inputs> |
79 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> | 76 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> |
80 <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" /> | 77 <param name="locustag" type="text" value="" label="Locus tag prefix (--locustag)" /> |
81 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" /> | 78 <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" /> |
82 <param name="gffver" type="select" label="GFF version (--gffver)"> | 79 <param name="gffver" type="select" label="GFF version (--gffver)"> |
83 <option value="3">3</option> | 80 <option value="3">3</option> |
84 <option value="2">2</option> | 81 <option value="2">2</option> |
85 <option value="1">1</option> | 82 <option value="1">1</option> |
137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option> | 134 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option> |
138 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option> | 135 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option> |
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. (.sqn)</option> | 136 <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. (.sqn)</option> |
140 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option> | 137 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option> |
141 <option value="tbl" selected="True">Feature Table file (.tbl)</option> | 138 <option value="tbl" selected="True">Feature Table file (.tbl)</option> |
139 <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option> | |
142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option> | 140 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option> |
143 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option> | 141 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option> |
144 </param> | 142 </param> |
145 | 143 |
146 </inputs> | 144 </inputs> |
166 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa"> | 164 <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa"> |
167 <filter>outputs and 'fsa' in outputs</filter> | 165 <filter>outputs and 'fsa' in outputs</filter> |
168 </data> | 166 </data> |
169 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl"> | 167 <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl"> |
170 <filter>outputs and 'tbl' in outputs</filter> | 168 <filter>outputs and 'tbl' in outputs</filter> |
169 </data> | |
170 <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv"> | |
171 <filter>outputs and 'tsv' in outputs</filter> | |
171 </data> | 172 </data> |
172 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err"> | 173 <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err"> |
173 <filter>outputs and 'err' in outputs</filter> | 174 <filter>outputs and 'err' in outputs</filter> |
174 </data> | 175 </data> |
175 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt"> | 176 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt"> |
178 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" /> | 179 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" /> |
179 </outputs> | 180 </outputs> |
180 <tests> | 181 <tests> |
181 <test> | 182 <test> |
182 <param name="input" ftype="fasta" value="phiX174.fasta" /> | 183 <param name="input" ftype="fasta" value="phiX174.fasta" /> |
183 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" /> | 184 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" /> |
184 <output name="out_gff" file="out.gff" /> | 185 <output name="out_gff" file="out.gff" /> |
185 <output name="out_gbk" file="out.gbk" lines_diff="14" /> | 186 <output name="out_gbk" file="out.gbk" lines_diff="14" /> |
186 <output name="out_fna" file="out.fna" /> | 187 <output name="out_fna" file="out.fna" /> |
187 <output name="out_faa" file="out.faa" /> | 188 <output name="out_faa" file="out.faa" /> |
188 <output name="out_ffn" file="out.ffn" /> | 189 <output name="out_ffn" file="out.ffn" /> |
189 <output name="out_sqn" file="out.sqn" lines_diff="84" /> | 190 <output name="out_sqn" file="out.sqn" lines_diff="84" /> |
190 <output name="out_fsa" file="out.fsa" /> | 191 <output name="out_fsa" file="out.fsa" /> |
191 <output name="out_tbl" file="out.tbl" /> | 192 <output name="out_tbl" file="out.tbl" /> |
193 <output name="out_tsv" file="out.tsv" /> | |
192 <output name="out_err" file="out.err" /> | 194 <output name="out_err" file="out.err" /> |
193 <output name="out_txt" file="out.txt" /> | 195 <output name="out_txt" file="out.txt" /> |
194 <output name="out_log"> | 196 <output name="out_log"> |
195 <assert_contents> | 197 <assert_contents> |
196 <has_text text="Type 'prokka --citation' for more details." /> | 198 <has_text text="Type 'prokka --citation' for more details." /> |
209 | 211 |
210 Prokka creates several output files, which are described in the **Additional outputs** section above. | 212 Prokka creates several output files, which are described in the **Additional outputs** section above. |
211 | 213 |
212 **License and citation** | 214 **License and citation** |
213 | 215 |
214 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. | 216 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_. |
215 | 217 |
216 .. _CRS4 Srl.: http://www.crs4.it/ | 218 .. _CRS4 Srl.: http://www.crs4.it/ |
217 .. _Earlham Institute: http://earlham.ac.uk/ | 219 .. _Earlham Institute: http://earlham.ac.uk/ |
218 .. _MIT license: https://opensource.org/licenses/MIT | 220 .. _MIT license: https://opensource.org/licenses/MIT |
219 | 221 |