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planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner commit f7690d10e0515911ee00455806e457bc53f145c7-dirty
author greg
date Thu, 13 Jun 2024 11:54:31 +0000
parents 32587f12102c
children
comparison
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10:79ea0eef1942 11:1c5a484fc06f
1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0"> 1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@TOOL_VERSION@.4.0+galaxy0">
2 <description>aligns integrated orthologous gene family clusters</description> 2 <description>aligns integrated orthologous gene family clusters</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_aligner</requirement> 7 <requirement type="package" version="1.0.4">plant_tribes_gene_family_aligner</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #set alignment_method = $alignment_method_cond.alignment_method 10 #set alignment_method = $alignment_method_cond.alignment_method
11 #set input_dir = 'input_dir' 11 #set input_dir = 'input_dir'
12 mkdir $input_dir && 12 mkdir $input_dir &&
136 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" /> 136 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
137 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 137 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
138 </collection> 138 </collection>
139 </outputs> 139 </outputs>
140 <tests> 140 <tests>
141 <test> 141 <test expect_num_outputs="2">
142 <param name="input"> 142 <param name="input">
143 <collection type="list"> 143 <collection type="list">
144 <element name="3722.faa" value="3722.faa"/> 144 <element name="3722.faa" value="3722.faa"/>
145 <element name="3722.fna" value="3722.fna"/> 145 <element name="3722.fna" value="3722.fna"/>
146 <element name="38889.faa" value="38889.faa"/> 146 <element name="38889.faa" value="38889.faa"/>
149 <element name="39614.fna" value="39614.fna"/> 149 <element name="39614.fna" value="39614.fna"/>
150 </collection> 150 </collection>
151 </param> 151 </param>
152 <param name="codon_alignments" value="yes"/> 152 <param name="codon_alignments" value="yes"/>
153 <output_collection name="primary_faa" type="list"> 153 <output_collection name="primary_faa" type="list">
154 <element name="3722.faa.aln" file="3722.faa.aln" ftype="fasta"/> 154 <element name="3722.faa.aln" ftype="fasta">
155 <element name="38889.faa.aln" file="38889.faa.aln" ftype="fasta"/> 155 <assert_contents>
156 <element name="39614.faa.aln" file="39614.faa.aln" ftype="fasta"/> 156 <has_text text=">gnl_Glyma1.01_PACid_16266208"/>
157 <has_text text=">gnl_Vitvi12X_PACid_17827068"/>
158 <has_text text=">gnl_Selmo1.0_PACid_15401289"/>
159 <has_text text=">gnl_Orysa6.0_PACid_16864430"/>
160 <has_text text=">contig_7"/>
161 </assert_contents>
162 </element>
163 <element name="38889.faa.aln" ftype="fasta">
164 <assert_contents>
165 <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
166 <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
167 <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
168 <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
169 <has_text text=">contig_2"/>
170 </assert_contents>
171 </element>
172 <element name="39614.faa.aln" ftype="fasta">
173 <assert_contents>
174 <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
175 <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
176 <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
177 <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
178 <has_text text=">contig_3"/>
179 </assert_contents>
180 </element>
157 </output_collection> 181 </output_collection>
158 <output_collection name="primary_fna" type="list"> 182 <output_collection name="primary_fna" type="list">
159 <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/> 183 <element name="3722.fna.aln" ftype="fasta">
160 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/> 184 <assert_contents>
161 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/> 185 <has_text text=">gnl_Glyma1.01_PACid_16266208"/>
186 <has_text text=">gnl_Glyma1.01_PACid_16266209"/>
187 <has_text text=">gnl_Glyma1.01_PACid_16266210"/>
188 <has_text text=">gnl_Glyma1.01_PACid_16301083"/>
189 <has_text text=">contig_7"/>
190 </assert_contents>
191 </element>
192 <element name="38889.fna.aln" ftype="fasta">
193 <assert_contents>
194 <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
195 <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
196 <has_text text=">gnl_Mimgu1.0_PACid_17675619"/>
197 <has_text text=">gnl_Solly2.3_Solyc06g053200.2.1"/>
198 <has_text text=">contig_2"/>
199 </assert_contents>
200 </element>
201 <element name="39614.fna.aln" ftype="fasta">
202 <assert_contents>
203 <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
204 <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
205 <has_text text=">gnl_Orysa6.0_PACid_16878968"/>
206 <has_text text=">gnl_Phoda3.0_PDK_30s1023721g001"/>
207 <has_text text=">contig_3"/>
208 </assert_contents>
209 </element>
162 </output_collection> 210 </output_collection>
163 </test> 211 </test>
164 </tests> 212 </tests>
165 <help> 213 <help>
166 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 214 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
197 245
198 .. _trimAl: http://trimal.cgenomics.org 246 .. _trimAl: http://trimal.cgenomics.org
199 247
200 </help> 248 </help>
201 <citations> 249 <citations>
202 <expand macro="citation1" /> 250 <citation type="doi">10.3389/fpls.2022.1011199</citation>
203 <citation type="bibtex"> 251 <citation type="doi">10.1371/journal.pone.0146062</citation>
204 @article{Wall2008, 252 <citation type="doi">10.1038/nprot.2013.084</citation>
205 journal = {Nucleic Acids Research}, 253 <citation type="doi">10.1101/gr.9.9.868</citation>
206 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS}, 254 <citation type="doi">10.1142/9781848165632_0019</citation>
207 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants}, 255 <citation type="doi">10.1093/molbev/mst010</citation>
208 year = {2008}, 256 <citation type="doi">10.1093/nar/gks631</citation>
209 volume = {36}, 257 <citation type="doi">10.1101/gr.1224503</citation>
210 number = {suppl 1}, 258 <citation type="doi">10.1186/s13059-015-0721-2</citation>
211 pages = {D970-D976},} 259 <citation type="doi">10.1093/bioinformatics/btp348</citation>
212 </citation> 260 <citation type="doi">10.1109/TCBB.2013.68</citation>
213 <citation type="bibtex">
214 @article{Katoh2013,
215 journal = {Molecular biology and evolution},
216 author = {3. Katoh K, Standley DM},
217 title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
218 year = {2013},
219 volume = {30},
220 number = {4},
221 pages = {772-780},}
222 </citation>
223 <citation type="bibtex">
224 @article{Mirarab2014,
225 journal = {Research in Computational Molecular Biology (RECOMB)},
226 author = {4. Mirarab S, Nguyen N, Warnow T},
227 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
228 year = {2014},
229 pages = {177–191},
230 url = {https://github.com/smirarab/pasta},}
231 </citation>
232 <citation type="bibtex">
233 @article{Capella-Gutierrez2009,
234 journal = {Bioinformatics,},
235 author = {5. Capella-Gutierrez S, Silla-Martínez JM, Gabaldón T},
236 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
237 year = {2009},
238 volume = {25},
239 number = {15},
240 pages = {1972-1973},}
241 </citation>
242 <citation type="bibtex">
243 @article{Yachdav2016,
244 journal = {Bioinformatics,},
245 author = {6. Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T},
246 title = {MSAViewer: interactive JavaScript visualization of multiple sequence alignments},
247 year = {2016},
248 volume = {32},
249 number = {22},
250 pages = {3501-3503},}
251 </citation>
252 <citation type="bibtex">
253 @article{Clamp2004,
254 journal = {Bioinformatics,},
255 author = {7. Clamp M, Cuff J, Searle SM, Barton GJ},
256 title = {The jalview java alignment editor},
257 year = {2004},
258 volume = {20},
259 number = {3},
260 pages = {426-427},}
261 </citation>
262 </citations> 261 </citations>
263 </tool> 262 </tool>