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comparison prokka.xml @ 11:fd4b2f03cfc6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit b391e22790013f0eebed85685b194c39ffcf17d8
author iuc
date Sat, 29 Oct 2016 09:29:09 -0400
parents 392255fa7ab9
children da479161bbe4
comparison
equal deleted inserted replaced
10:6aa88a432ffc 11:fd4b2f03cfc6
128 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" /> 128 <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
129 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" /> 129 <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
130 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> 130 <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
131 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> 131 <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
132 132
133 <param name="outputs" type="select" multiple="true" label="Additional outputs"> 133 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</option> 134 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
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> 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 (.gbk)</option>
136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option> 136 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
137 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option> 137 <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</option> 138 <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.</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>
140 <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</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>
141 <option value="tbl" selected="True">Feature Table file</option> 141 <option value="tbl" selected="True">Feature Table file (.tbl)</option>
142 <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option> 142 <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</option> 143 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
144 </param> 144 </param>
145 145
146 </inputs> 146 </inputs>
147 <outputs> 147 <outputs>
148 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff"> 148 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
205 205
206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 206 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
207 207
208 **Output files** 208 **Output files**
209 209
210 Prokka creates several output files: 210 Prokka creates several output files, which are described in the **Additional outputs** section above.
211
212 gff
213 This is the master annotation in GFF format, containing both sequences and annotations
214 gbk
215 This is a standard GenBank file derived from the master .gff . If the input to prokka was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence
216 fna
217 Nucleotide FASTA file of the input contig sequences
218 faa
219 Protein FASTA file of the translated CDS sequences
220 ffn
221 Nucleotide FASTA file of all the annotated sequences, not just CDS
222 sqn
223 An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc.
224 fsa
225 Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines
226 tbl
227 Feature Table file, used by "tbl2asn" to create the .sqn file
228 err
229 Unacceptable annotations - the NCBI discrepancy report
230 log
231 Contains all the output that Prokka produced during its run
232 txt
233 Statistics relating to the annotated features found
234 211
235 **License and citation** 212 **License and citation**
236 213
237 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. 214 This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
238 215