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planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 5b19bd262023af92bc9aaa65f75b5ec81814e90f-dirty
author greg
date Wed, 12 Jun 2024 19:29:25 +0000
parents 4d73965d99a2
children
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10:4d73965d99a2 11:2c2ad8af0a4e
1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.4.0" profile="18.09"> 1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@TOOL_VERSION@.4.0+galaxy0" profile="18.09">
2 <description>post-processes de novo transcriptome assembly</description> 2 <description>post-processes de novo transcriptome assembly</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
116 </data> 116 </data>
117 <data name="output_cleaned_cds" format="fasta" label="transcripts.cleaned.cds: ${tool.name} on ${on_string}"/> 117 <data name="output_cleaned_cds" format="fasta" label="transcripts.cleaned.cds: ${tool.name} on ${on_string}"/>
118 <data name="output_cds" format="fasta" label="transcripts.cds: ${tool.name} on ${on_string}"/> 118 <data name="output_cds" format="fasta" label="transcripts.cds: ${tool.name} on ${on_string}"/>
119 </outputs> 119 </outputs>
120 <tests> 120 <tests>
121 <test> 121 <test expect_num_outputs="4">
122 <param name="input" value="assembly.fasta" ftype="fasta"/> 122 <param name="input" value="assembly.fasta" ftype="fasta"/>
123 <output name="output_cds" file="transcripts.cds" ftype="fasta"/> 123 <output name="output_cds" file="transcripts.cds" ftype="fasta"/>
124 <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/> 124 <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/>
125 <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/> 125 <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/>
126 <output name="output_pep" file="transcripts.pep" ftype="fasta"/> 126 <output name="output_pep" file="transcripts.pep" ftype="fasta"/>
127 </test> 127 </test>
128 <test> 128 <test expect_num_outputs="8">
129 <param name="input" value="assembly_tgf.fasta" ftype="fasta"/> 129 <param name="input" value="assembly_tgf.fasta" ftype="fasta"/>
130 <param name="options_type_selector" value="advanced"/> 130 <param name="options_type_selector" value="advanced"/>
131 <param name="target_gene_family_assembly" value="yes"/> 131 <param name="target_gene_family_assembly" value="yes"/>
132 <param name="orthogroups" value="target_orthos.ids"/> 132 <param name="orthogroups" value="target_orthos.ids"/>
133 <param name="method" value="orthomcl"/> 133 <param name="method" value="orthomcl"/>
134 <param name="dereplicate" value="yes"/> 134 <param name="dereplicate" value="yes"/>
135 <output_collection name="output_targeted_gene_families" type="list"> 135 <output_collection name="output_targeted_gene_families" type="list" count="0">
136 </output_collection> 136 </output_collection>
137 <output name="output_targeted_gene_families_stats" file="output_targeted_gene_families_stats.tabular" ftype="tabular"/> 137 <output name="output_targeted_gene_families_stats" file="output_targeted_gene_families_stats.tabular" ftype="tabular"/>
138 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/> 138 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/>
139 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/> 139 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/>
140 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/> 140 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/>
172 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12]. 172 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
173 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp. 173 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
174 174
175 </help> 175 </help>
176 <citations> 176 <citations>
177 <expand macro="citation1" /> 177 <citation type="doi">10.3389/fpls.2022.1011199</citation>
178 <citation type="bibtex"> 178 <citation type="doi">10.1371/journal.pone.0146062</citation>
179 @article{Honaas2016, 179 <citation type="doi">10.1038/nprot.2013.084</citation>
180 journal = {PloS one}, 180 <citation type="doi">10.1101/gr.9.9.868</citation>
181 author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH}, 181 <citation type="doi">10.1142/9781848165632_0019</citation>
182 title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome}, 182 <citation type="doi">10.1093/molbev/mst010</citation>
183 year = {2016}, 183 <citation type="doi">10.1093/nar/gks631</citation>
184 volume = {11}, 184 <citation type="doi">10.1101/gr.1224503</citation>
185 number = {1}, 185 <citation type="doi">10.1186/s13059-015-0721-2</citation>
186 pages = {e0146062},} 186 <citation type="doi">10.1093/bioinformatics/btp348</citation>
187 </citation> 187 <citation type="doi">10.1109/TCBB.2013.68</citation>
188 <citation type="bibtex">
189 @article{Haas2013,
190 journal = {Nature Protocols},
191 author = {3. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD},
192 title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis},
193 year = {2013},
194 volume = {8},
195 number = {8},
196 pages = {1494-1512},}
197 </citation>
198 <citation type="bibtex">
199 @article{Huang1999,
200 journal = {Genome Research},
201 author = {5. Huang X, Madan A},
202 title = {CAP3: A DNA sequence assembly program},
203 year = {1999},
204 volume = {9},
205 number = {9},
206 pages = {868-877},
207 url = {http://seq.cs.iastate.edu/cap3.html},}
208 </citation>
209 <citation type="bibtex">
210 @article{Eddy2009,
211 journal = {Genome Inform},
212 author = {6. Eddy SR},
213 title = {A new generation of homology search tools based on probabilistic inference},
214 year = {2009},
215 volume = {23},
216 number = {1},
217 pages = {205-211},}
218 </citation>
219 <citation type="bibtex">
220 @article{Katoh2013,
221 journal = {Molecular biology and evolution},
222 author = {7. Katoh K, Standley DM},
223 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
224 year = {2013},
225 volume = {30},
226 number = {4},
227 pages = {772-780},}
228 </citation>
229 <citation type="bibtex">
230 @article{Sasidharan2012,
231 journal = {Nucleic Acids Research},
232 author = {8. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
233 title = {GFam: a platform for automatic annotation of gene families},
234 year = {2012},
235 pages = {gks631},}
236 </citation>
237 <citation type="bibtex">
238 @article{Li2003,
239 journal = {Genome Research}
240 author = {9. Li L, Stoeckert CJ, Roos DS},
241 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
242 year = {2003},
243 volume = {13},
244 number = {9},
245 pages = {2178-2189},}
246 </citation>
247 <citation type="bibtex">
248 @article{Emms2015,
249 journal = {Genome Biology}
250 author = {10. Emms DM, Kelly S},
251 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
252 year = {2015},
253 volume = {16},
254 number = {1},
255 pages = {157},}
256 </citation>
257 <citation type="bibtex">
258 @article{Capella-Gutierrez2009,
259 journal = {Bioinformatics,},
260 author = {11. Capella-Gutierrez S, Silla-Martínez JM, Gabaldón T},
261 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
262 year = {2009},
263 volume = {25},
264 number = {15},
265 pages = {1972-1973},}
266 </citation>
267 <citation type="bibtex">
268 @article{Gremme2013,
269 journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
270 author = {12. Gremme G, Steinbiss S, Kurtz S},
271 title = {GenomeTools: a comprehensive software library for efficient processing of structured genome annotations},
272 year = {2013},
273 volume = {10},
274 number = {3},
275 pages = {645-656},}
276 </citation>
277 </citations> 188 </citations>
278 </tool> 189 </tool>