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comparison prokka.xml @ 19:8a22554cdde2 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
author iuc
date Tue, 16 Nov 2021 18:59:22 +0000
parents d643e3b03500
children
comparison
equal deleted inserted replaced
18:d643e3b03500 19:8a22554cdde2
1 <tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Prokaryotic genome annotation</description> 2 <description>Prokaryotic genome annotation</description>
3 <xrefs>
4 <xref type="bio.tools">prokka</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@TOOL_VERSION@">1.14.6</token> 7 <token name="@TOOL_VERSION@">1.14.6</token>
5 <token name="@VERSION_SUFFIX@">0</token> 8 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 9 </macros>
7 <requirements> 10 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">prokka</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">prokka</requirement>
9 </requirements> 12 </requirements>
10 13
130 <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" /> 133 <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
131 <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" /> 134 <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" />
132 <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> 135 <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
133 <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> 136 <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
134 137
135 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs"> 138 <param name="outputs" type="select" multiple="true" label="Additional outputs">
136 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option> 139 <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
137 <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> 140 <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>
138 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option> 141 <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
139 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option> 142 <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
140 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option> 143 <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
146 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option> 149 <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
147 </param> 150 </param>
148 151
149 </inputs> 152 </inputs>
150 <outputs> 153 <outputs>
151 <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff"> 154 <data name="out_gff" format="gff3" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
152 <filter>outputs and 'gff' in outputs</filter> 155 <filter>outputs and 'gff' in outputs</filter>
153 </data> 156 </data>
154 <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk"> 157 <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
155 <filter>outputs and 'gbk' in outputs</filter> 158 <filter>outputs and 'gbk' in outputs</filter>
156 </data> 159 </data>
185 </outputs> 188 </outputs>
186 <tests> 189 <tests>
187 <test> 190 <test>
188 <param name="input" ftype="fasta" value="phiX174.fasta" /> 191 <param name="input" ftype="fasta" value="phiX174.fasta" />
189 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" /> 192 <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" />
190 <output name="out_gff" file="out.gff" /> 193 <output name="out_gff" file="out.gff" ftype="gff3" />
191 <output name="out_gbk" > 194 <output name="out_gbk" >
192 <assert_contents> 195 <assert_contents>
193 <has_text_matching expression="LOCUS" /> 196 <has_text_matching expression="LOCUS" />
194 <has_text_matching expression="//" /> 197 <has_text_matching expression="//" />
195 </assert_contents> 198 </assert_contents>
196 </output> 199 </output>
197 <output name="out_fna" file="out.fna" /> 200 <output name="out_fna" file="out.fna" ftype="fasta" />
198 <output name="out_faa" file="out.faa" /> 201 <output name="out_faa" file="out.faa" ftype="fasta" />
199 <output name="out_ffn" file="out.ffn" /> 202 <output name="out_ffn" file="out.ffn" ftype="fasta" />
200 <output name="out_sqn" > 203 <output name="out_sqn" >
201 <assert_contents> 204 <assert_contents>
202 <has_text_matching expression="Seq-entry" /> 205 <has_text_matching expression="Seq-entry" />
203 <has_text_matching expression="contig2" /> 206 <has_text_matching expression="contig2" />
204 </assert_contents> 207 </assert_contents>
205 </output> 208 </output>
206 <output name="out_fsa" file="out.fsa" /> 209 <output name="out_fsa" file="out.fsa" ftype="fasta" />
207 <output name="out_tbl" file="out.tbl" /> 210 <output name="out_tbl" file="out.tbl" ftype="txt" />
208 <output name="out_tsv" file="out.tsv" /> 211 <output name="out_tsv" file="out.tsv" ftype="tabular" />
209 <output name="out_err" file="out.err" lines_diff="14" /> 212 <output name="out_err" file="out.err" lines_diff="14" ftype="txt" />
210 <output name="out_txt" file="out.txt" /> 213 <output name="out_txt" file="out.txt" ftype="txt" />
211 <output name="out_log"> 214 <output name="out_log">
212 <assert_contents> 215 <assert_contents>
213 <has_text text="Type 'prokka --citation' for more details." /> 216 <has_text text="Type 'prokka --citation' for more details." />
214 </assert_contents> 217 </assert_contents>
215 </output> 218 </output>