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comparison prokka.xml @ 13:a17498c603ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
author iuc
date Tue, 21 Mar 2017 10:13:06 -0400
parents da479161bbe4
children eaee459f3d69
comparison
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12:da479161bbe4 13:a17498c603ec
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>