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comparison kaks_analysis.xml @ 45:eaf9663f0cb0 draft

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author greg
date Tue, 24 Oct 2017 10:02:26 -0400
parents c877a0c9e224
children e3b41d2889d4
comparison
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44:c877a0c9e224 45:eaf9663f0cb0
65 #end if 65 #end if
66 >/dev/null 66 >/dev/null
67 && mv $output_dir/species1.fna '$output_species1_fna' 67 && mv $output_dir/species1.fna '$output_species1_fna'
68 && mv $output_dir/species1.faa '$output_species1_faa' 68 && mv $output_dir/species1.faa '$output_species1_faa'
69 #if str($comparison) == 'paralogs': 69 #if str($comparison) == 'paralogs':
70 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_para_ortho' 70 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
71 && mv $output_dir/*.rbhb '$output_rbhb_paralog'
71 #else: 72 #else:
72 && mv $output_dir/species2.faa '$output_species2_faa' 73 && mv $output_dir/species2.faa '$output_species2_faa'
73 && mv $output_dir/species2.fna '$output_species2_fna' 74 && mv $output_dir/species2.fna '$output_species2_fna'
74 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_para_ortho' 75 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
75 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' 76 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
76 #end if 77 && mv $output_dir/*.rbhb '$output_rbhb_ortholog'
77 && mv $output_dir/*.rbhb '$output_rbhb' 78 #end if
78 && mv $output_dir/*.kaks '$output_kaks' 79 && mv $output_dir/*.kaks '$output_kaks'
79 #if str($fit_components) == 'yes': 80 #if str($fit_components) == 'yes':
80 && mv $output_dir/*.components '$output_components' 81 && mv $output_dir/*.components '$output_components'
81 #end if 82 #end if
82 ]]></command> 83 ]]></command>
179 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 180 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
180 </data> 181 </data>
181 <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids species2) on ${on_string}"> 182 <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids species2) on ${on_string}">
182 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 183 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
183 </data> 184 </data>
184 <data name="output_species1_para_ortho" format="tabular" label="${tool.name} (blastn results species1 vs species1) on ${on_string}"> 185 <data name="output_species1_paralog" format="tabular" label="${tool.name} (blastn results species1 vs species1) on ${on_string}">
185 <filter>comparison_cond['comparison'] == 'paralogs'</filter> 186 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
186 </data> 187 </data>
187 <data name="output_species1_para_ortho" format="tabular" label="${tool.name} (blastn results species1 vs species2) on ${on_string}"> 188 <data name="output_species1_ortholog" format="tabular" label="${tool.name} (blastn results species1 vs species2) on ${on_string}">
188 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 189 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
189 </data> 190 </data>
190 <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results species2 vs species1) on ${on_string}"> 191 <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results species2 vs species1) on ${on_string}">
191 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 192 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
192 </data> 193 </data>
193 <data name="output_rbhb" format="tabular" label="${tool.name} (paralogous pairs) on ${on_string}"> 194 <data name="output_rbhb_paralog" format="tabular" label="${tool.name} (paralogous pairs) on ${on_string}">
194 <filter>comparison_cond['comparison'] == 'paralogs'</filter> 195 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
195 </data> 196 </data>
196 <data name="output_rbhb" format="tabular" label="${tool.name} (orthologous pairs) on ${on_string}"> 197 <data name="output_rbhb_ortholog" format="tabular" label="${tool.name} (orthologous pairs) on ${on_string}">
197 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 198 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
198 </data> 199 </data>
199 <data name="output_kaks" format="tabular" label="${tool.name} (KaKs distribution) on ${on_string}" /> 200 <data name="output_kaks" format="tabular" label="${tool.name} (KaKs distribution) on ${on_string}" />
200 <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the KaKs distribution) on ${on_string}"> 201 <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the KaKs distribution) on ${on_string}">
201 <filter>options_type['options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes'</filter> 202 <filter>options_type['options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes'</filter>
206 <param name="coding_sequences_species_1" value="species1_cds.fasta" ftype="fasta"/> 207 <param name="coding_sequences_species_1" value="species1_cds.fasta" ftype="fasta"/>
207 <param name="proteins_species_1" value="species1_pep.fasta" ftype="fasta"/> 208 <param name="proteins_species_1" value="species1_pep.fasta" ftype="fasta"/>
208 <param name="non_commercial_use" value="True"/> 209 <param name="non_commercial_use" value="True"/>
209 <output name="output_species1_fna" file="species1_cds.fasta" ftype="fasta" compare="contains"/> 210 <output name="output_species1_fna" file="species1_cds.fasta" ftype="fasta" compare="contains"/>
210 <output name="output_species1_faa" file="species1_pep.fasta" ftype="fasta" compare="contains"/> 211 <output name="output_species1_faa" file="species1_pep.fasta" ftype="fasta" compare="contains"/>
211 <output name="output_species1_para_ortho" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/> 212 <output name="output_species1_paralog" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/>
212 <output name="output_rbhb" file="output_paralogous_pairs.tabular" ftype="tabular"/> 213 <output name="output_rbhb_paralog" file="output_paralogous_pairs.tabular" ftype="tabular"/>
213 <output name="output_kaks" file="output1.tabular" ftype="tabular"/> 214 <output name="output_kaks" file="output1.tabular" ftype="tabular"/>
214 </test> 215 </test>
215 </tests> 216 </tests>
216 <help> 217 <help>
217 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses 218 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses