Mercurial > repos > crs4 > prokka
comparison prokka.xml @ 19:8a22554cdde2 draft default tip
"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 |
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| 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> |