Mercurial > repos > crs4 > prokka
comparison prokka.xml @ 13:a17498c603ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
author | iuc |
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date | Tue, 21 Mar 2017 10:13:06 -0400 |
parents | da479161bbe4 |
children | eaee459f3d69 |
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12:da479161bbe4 | 13:a17498c603ec |
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1 <tool id="prokka" name="Prokka" version="1.11.1"> | 1 <tool id="prokka" name="Prokka" version="1.12.0"> |
2 <description>prokaryotic genome annotation</description> | 2 <description>prokaryotic genome annotation</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.11">prokka</requirement> | 4 <requirement type="package" version="1.12">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 <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> |
7 <stdio> | 7 <stdio> |
8 <exit_code range="1:" /> | 8 <exit_code range="1:" /> |
9 </stdio> | 9 </stdio> |
187 <output name="out_faa" file="out.faa" /> | 187 <output name="out_faa" file="out.faa" /> |
188 <output name="out_ffn" file="out.ffn" /> | 188 <output name="out_ffn" file="out.ffn" /> |
189 <output name="out_sqn" file="out.sqn" lines_diff="84" /> | 189 <output name="out_sqn" file="out.sqn" lines_diff="84" /> |
190 <output name="out_fsa" file="out.fsa" /> | 190 <output name="out_fsa" file="out.fsa" /> |
191 <output name="out_tbl" file="out.tbl" /> | 191 <output name="out_tbl" file="out.tbl" /> |
192 <output name="out.err" file="out.err" /> | 192 <output name="out_err" file="out.err" /> |
193 <output name="out_txt" file="out.txt" /> | 193 <output name="out_txt" file="out.txt" /> |
194 <output name="out_log"> | 194 <output name="out_log"> |
195 <assert_contents> | 195 <assert_contents> |
196 <has_text text="Type 'prokka --citation' for more details." /> | 196 <has_text text="Type 'prokka --citation' for more details." /> |
197 </assert_contents> | 197 </assert_contents> |
201 <help><![CDATA[ | 201 <help><![CDATA[ |
202 **What it does** | 202 **What it does** |
203 | 203 |
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. | 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. |
205 | 205 |
206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml | 206 .. _Prokka: http://github.com/tseemann/prokka |
207 | 207 |
208 **Output files** | 208 **Output files** |
209 | 209 |
210 Prokka creates several output files, which are described in the **Additional outputs** section above. | 210 Prokka creates several output files, which are described in the **Additional outputs** section above. |
211 | 211 |
217 .. _Earlham Institute: http://earlham.ac.uk/ | 217 .. _Earlham Institute: http://earlham.ac.uk/ |
218 .. _MIT license: https://opensource.org/licenses/MIT | 218 .. _MIT license: https://opensource.org/licenses/MIT |
219 | 219 |
220 You can use this tool only if you agree to the license terms of: `Prokka`_. | 220 You can use this tool only if you agree to the license terms of: `Prokka`_. |
221 | 221 |
222 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml | 222 .. _Prokka: http://github.com/tseemann/prokka |
223 ]]></help> | 223 ]]></help> |
224 <citations> | 224 <citations> |
225 <citation type="doi">10.1093/bioinformatics/btu135</citation> | 225 <citation type="doi">10.1093/bioinformatics/btu135</citation> |
226 <citation type="doi">10.1093/bioinformatics/btu153</citation> | 226 <citation type="doi">10.1093/bioinformatics/btu153</citation> |
227 </citations> | 227 </citations> |