Mercurial > repos > iuc > funannotate_annotate

comparison funannotate_annotate.xml @ 10:d0336d67702b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 737d7e9a31c9d340a38ddfef3ac20847989718e0
author iuc
date Sun, 11 Feb 2024 00:08:00 +0000
parents 3bbe70fef6df
children 9c15ca7e764e
comparison
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9:3bbe70fef6df 10:d0336d67702b
1 <tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy5">
2 <description>annotation</description> 2 <description>annotation</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="biotools" /> 6 <expand macro="biotools" />
70 --header_length $header_length 70 --header_length $header_length
71 --cpus \${GALAXY_SLOTS:-2} 71 --cpus \${GALAXY_SLOTS:-2}
72 72
73 && 73 &&
74 74
75 ## funannotate sometimes leaves multiple *part.tbl and *part.sqn files 75 ## Funannotate sometimes leaves multiple *part.tbl and *part.sqn files:
76 ## https://github.com/nextgenusfs/funannotate/issues/777 76 ## https://github.com/nextgenusfs/funannotate/issues/777
77 ## The partial tbl files are combined by funannotate and are deleted below.
78 ## The sqn files are discrete and are collected with discover_datasets.
77 find output/annotate_results 79 find output/annotate_results
78 -regex ".*part_[0-9]+\.\(sqn\|tbl\)$" 80 -regex ".*part_[0-9]+\.\(tbl\)$"
79 -delete 81 -delete
80 82
81 &&
82
83 mv output/annotate_results/*.gbk out.gbk &&
84 mv output/annotate_results/*.annotations.txt out.annotations.txt &&
85 mv output/annotate_results/*.contigs.fsa out.contigs.fsa &&
86 mv output/annotate_results/*.agp out.agp &&
87 mv output/annotate_results/*.tbl out.tbl &&
88 mv output/annotate_results/*.sqn out.sqn &&
89 mv output/annotate_results/*.scaffolds.fa out.scaffolds.fa &&
90 mv output/annotate_results/*.proteins.fa out.proteins.fa &&
91 mv output/annotate_results/*.mrna-transcripts.fa out.mrna-transcripts.fa &&
92 mv output/annotate_results/*.cds-transcripts.fa out.cds-transcripts.fa &&
93 mv output/annotate_results/*.gff3 out.gff3 &&
94 mv output/annotate_results/*.discrepency.report.txt out.discrepency.report.txt &&
95 mv output/annotate_results/*.stats.json out.stats.json
96 ]]></command> 83 ]]></command>
97 <inputs> 84 <inputs>
98 85
99 <conditional name="input"> 86 <conditional name="input">
100 <param name="input_type" type="select" label="Input format"> 87 <param name="input_type" type="select" label="Input format">
162 <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option> 149 <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option>
163 <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option> 150 <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option>
164 </param> 151 </param>
165 </inputs> 152 </inputs>
166 <outputs> 153 <outputs>
167 <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk"> 154 <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="output/annotate_results/*.gbk">
168 <filter>outputs and 'gbk' in outputs</filter> 155 <filter>outputs and 'gbk' in outputs</filter>
169 </data> 156 </data>
170 <data name='annot' format='tabular' label="${tool.name} on ${on_string}: all annotations" from_work_dir="out.annotations.txt"> 157 <data name='annot' format='tabular' label="${tool.name} on ${on_string}: all annotations" from_work_dir="output/annotate_results/*.annotations.txt">
171 <filter>outputs and 'annotations' in outputs</filter> 158 <filter>outputs and 'annotations' in outputs</filter>
172 </data> 159 </data>
173 <data name='contigs_fsa' format='fasta' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="out.contigs.fsa"> 160 <data name='contigs_fsa' format='fasta' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="output/annotate_results/*.contigs.fsa">
174 <filter>outputs and 'contigs_fsa' in outputs</filter> 161 <filter>outputs and 'contigs_fsa' in outputs</filter>
175 </data> 162 </data>
176 <data name='agp' format='tabular' label="${tool.name} on ${on_string}: AGP file" from_work_dir="out.agp"> 163 <data name='agp' format='tabular' label="${tool.name} on ${on_string}: AGP file" from_work_dir="output/annotate_results/*.agp">
177 <filter>outputs and 'agp' in outputs</filter> 164 <filter>outputs and 'agp' in outputs</filter>
178 </data> 165 </data>
179 <data name='tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl"> 166 <data name='tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="output/annotate_results/*.tbl">
180 <filter>outputs and 'tbl' in outputs</filter> 167 <filter>outputs and 'tbl' in outputs</filter>
181 </data> 168 </data>
182 <data name='sqn' format='txt' label="${tool.name} on ${on_string}: NCBI Sequin genome" from_work_dir="out.sqn"> 169 <collection name="sqn" type="list" label="${tool.name} on ${on_string}: NCBI Sequin genome files">
170 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sqn" directory="output/annotate_results" format="txt" recurse="false"/>
183 <filter>outputs and 'sqn' in outputs</filter> 171 <filter>outputs and 'sqn' in outputs</filter>
184 </data> 172 </collection>
185 <data name='fa_scaffolds' format='fasta' label="${tool.name} on ${on_string}: scaffolds sequences" from_work_dir="out.scaffolds.fa"> 173 <data name='fa_scaffolds' format='fasta' label="${tool.name} on ${on_string}: scaffolds sequences" from_work_dir="output/annotate_results/*.scaffolds.fa">
186 <filter>outputs and 'scaffolds_fa' in outputs</filter> 174 <filter>outputs and 'scaffolds_fa' in outputs</filter>
187 </data> 175 </data>
188 <data name='fa_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa"> 176 <data name='fa_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="output/annotate_results/*.proteins.fa">
189 <filter>outputs and 'proteins_fa' in outputs</filter> 177 <filter>outputs and 'proteins_fa' in outputs</filter>
190 </data> 178 </data>
191 <data name='fa_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa"> 179 <data name='fa_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="output/annotate_results/*.mrna-transcripts.fa">
192 <filter>outputs and 'mrna_transcripts_fa' in outputs</filter> 180 <filter>outputs and 'mrna_transcripts_fa' in outputs</filter>
193 </data> 181 </data>
194 <data name='fa_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa"> 182 <data name='fa_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="output/annotate_results/*.cds-transcripts.fa">
195 <filter>outputs and 'cds_transcripts_fa' in outputs</filter> 183 <filter>outputs and 'cds_transcripts_fa' in outputs</filter>
196 </data> 184 </data>
197 <data name='gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3"> 185 <data name='gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="output/annotate_results/*.gff3">
198 <filter>outputs and 'gff3' in outputs</filter> 186 <filter>outputs and 'gff3' in outputs</filter>
199 </data> 187 </data>
200 <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt"> 188 <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="output/annotate_results/*.discrepency.report.txt">
201 <filter>outputs and 'discrepency' in outputs</filter> 189 <filter>outputs and 'discrepency' in outputs</filter>
202 </data> 190 </data>
203 <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json"> 191 <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="output/annotate_results/*.stats.json">
204 <filter>outputs and 'gbk' in outputs</filter> 192 <filter>outputs and 'gbk' in outputs</filter>
205 </data> 193 </data>
206 <data name='must_fix' format='json' label="${tool.name} on ${on_string}: Gene Name/Product must-fix" from_work_dir="output/annotate_results/Gene2Products.must-fix.txt"> 194 <data name='must_fix' format='json' label="${tool.name} on ${on_string}: Gene Name/Product must-fix" from_work_dir="output/annotate_results/Gene2Products.must-fix.txt">
207 <filter>outputs and 'must_fix' in outputs</filter> 195 <filter>outputs and 'must_fix' in outputs</filter>
208 </data> 196 </data>
246 <output name="tbl"> 234 <output name="tbl">
247 <assert_contents> 235 <assert_contents>
248 <has_text text="locus_tag" /> 236 <has_text text="locus_tag" />
249 </assert_contents> 237 </assert_contents>
250 </output> 238 </output>
251 <output name="sqn"> 239 <output_collection name="sqn" type="list">
252 <assert_contents> 240 <element name="Genus_species">
253 <has_text text="Seq-submit" /> 241 <assert_contents>
254 </assert_contents> 242 <has_text text="Seq-submit" />
255 </output> 243 </assert_contents>
244 </element>
245 </output_collection>
256 <output name="fa_scaffolds"> 246 <output name="fa_scaffolds">
257 <assert_contents> 247 <assert_contents>
258 <has_text text=">sample" /> 248 <has_text text=">sample" />
259 </assert_contents> 249 </assert_contents>
260 </output> 250 </output>
338 <output name="tbl"> 328 <output name="tbl">
339 <assert_contents> 329 <assert_contents>
340 <has_text text="locus_tag" /> 330 <has_text text="locus_tag" />
341 </assert_contents> 331 </assert_contents>
342 </output> 332 </output>
343 <output name="sqn"> 333 <output_collection name="sqn" type="list">
344 <assert_contents> 334 <element name="Genus_species">
345 <has_text text="Seq-submit" /> 335 <assert_contents>
346 </assert_contents> 336 <has_text text="Seq-submit" />
347 </output> 337 </assert_contents>
338 </element>
339 </output_collection>
348 <output name="fa_scaffolds"> 340 <output name="fa_scaffolds">
349 <assert_contents> 341 <assert_contents>
350 <has_text text=">sample" /> 342 <has_text text=">sample" />
351 </assert_contents> 343 </assert_contents>
352 </output> 344 </output>