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comparison kaks_analysis.xml @ 43:174a0fdda6bd draft

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Uploaded
author greg
date Tue, 24 Oct 2017 08:40:46 -0400
parents ec47f2f694e7
children c877a0c9e224
comparison
equal deleted inserted replaced
42:ec47f2f694e7 43:174a0fdda6bd
34 --proteins_species_1 '$proteins_species_1' 34 --proteins_species_1 '$proteins_species_1'
35 --comparison $comparison 35 --comparison $comparison
36 #if str($comparison) == 'orthologs': 36 #if str($comparison) == 'orthologs':
37 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2' 37 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
38 --proteins_species_2 '$comparison_cond.proteins_species_2' 38 --proteins_species_2 '$comparison_cond.proteins_species_2'
39 #set blast_option = $comparison_cond.blast_option 39 #if str($comparison_cond.blast_option) == 'crbblast':
40 #if str($blast_option) == 'crbblast':
41 --crb_blast 40 --crb_blast
42 #end if 41 #end if
43 #end if 42 #end if
44 #if str($options_type.options_type_selector) == 'advanced': 43 #if str($options_type.options_type_selector) == 'advanced':
45 #if str($set_min_coverage) == 'yes': 44 #if str($set_min_coverage) == 'yes':
66 #end if 65 #end if
67 >/dev/null 66 >/dev/null
68 && mv $output_dir/species1.fna '$output_species1_fna' 67 && mv $output_dir/species1.fna '$output_species1_fna'
69 && mv $output_dir/species1.faa '$output_species1_faa' 68 && mv $output_dir/species1.faa '$output_species1_faa'
70 #if str($comparison) == 'paralogs': 69 #if str($comparison) == 'paralogs':
71 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' 70 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_para_ortho'
72 #else: 71 #else:
73 && mv $output_dir/species2.faa '$output_species2_faa' 72 && mv $output_dir/species2.faa '$output_species2_faa'
74 && mv $output_dir/species2.fna '$output_species2_fna' 73 && mv $output_dir/species2.fna '$output_species2_fna'
75 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' 74 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_para_ortho'
76 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' 75 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
77 #end if 76 #end if
78 && mv $output_dir/*.rbhb '$output_rbhb' 77 && mv $output_dir/*.rbhb '$output_rbhb'
79 && mv $output_dir/*.kaks '$output_kaks' 78 && mv $output_dir/*.kaks '$output_kaks'
80 #if str($fit_components) == 'yes': 79 #if str($fit_components) == 'yes':
172 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> 171 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
173 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> 172 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
174 </param> 173 </param>
175 </inputs> 174 </inputs>
176 <outputs> 175 <outputs>
177 <data name="output_species1_fna" format="fasta" label="${tool.name} (coding sequences) on ${on_string}" /> 176 <data name="output_species1_fna" format="fasta" label="${tool.name} (coding sequences species1) on ${on_string}" />
178 <data name="output_species1_faa" format="fasta" label="${tool.name} (amino acids) on ${on_string}" /> 177 <data name="output_species1_faa" format="fasta" label="${tool.name} (amino acids species1) on ${on_string}" />
179 <data name="output_species2_fna" format="fasta" label="${tool.name} (coding sequences) on ${on_string}"> 178 <data name="output_species2_fna" format="fasta" label="${tool.name} (coding sequences species2) on ${on_string}">
180 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 179 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
181 </data> 180 </data>
182 <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids) on ${on_string}"> 181 <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids species2) on ${on_string}">
183 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 182 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
184 </data> 183 </data>
185 <data name="output_species1_paralog" format="tabular" label="${tool.name} (blastn results) on ${on_string}"> 184 <data name="output_species1_para_ortho" format="tabular" label="${tool.name} (blastn results species1 vs species2) on ${on_string}"/>
186 <filter>comparison_cond['comparison'] == 'paralogs'</filter> 185 <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results species2 vs species1) on ${on_string}">
187 </data>
188 <data name="output_species1_ortholog" format="tabular" label="${tool.name} (blastn results) on ${on_string}">
189 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 186 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
190 </data> 187 </data>
191 <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results) on ${on_string}"> 188 <data name="output_rbhb" format="tabular" label="${tool.name} (orthologous pairs) on ${on_string}" />
192 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 189 <data name="output_kaks" format="tabular" label="${tool.name} (KaKs distribution) on ${on_string}" />
193 </data> 190 <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the KaKs distribution) on ${on_string}">
194 <data name="output_rbhb" format="tabular" label="${tool.name} (paralogous pairs) on ${on_string}" />
195 <data name="output_kaks" format="tabular" label="${tool.name} on ${on_string}" />
196 <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the ks distribution) on ${on_string}">
197 <filter>options_type['options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes'</filter> 191 <filter>options_type['options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes'</filter>
198 </data> 192 </data>
199 </outputs> 193 </outputs>
200 <tests> 194 <tests>
201 <test> 195 <test>
202 <param name="coding_sequences_species_1" value="species1_cds.fasta" ftype="fasta"/> 196 <param name="coding_sequences_species_1" value="species1_cds.fasta" ftype="fasta"/>
203 <param name="proteins_species_1" value="species1_pep.fasta" ftype="fasta"/> 197 <param name="proteins_species_1" value="species1_pep.fasta" ftype="fasta"/>
204 <param name="non_commercial_use" value="True"/> 198 <param name="non_commercial_use" value="True"/>
205 <output name="output_species1_fna" file="species1_cds.fasta" ftype="fasta" compare="contains"/> 199 <output name="output_species1_fna" file="species1_cds.fasta" ftype="fasta" compare="contains"/>
206 <output name="output_species1_faa" file="species1_pep.fasta" ftype="fasta" compare="contains"/> 200 <output name="output_species1_faa" file="species1_pep.fasta" ftype="fasta" compare="contains"/>
207 <output name="output_species1_paralog" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/> 201 <output name="output_species1_para_ortho" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/>
208 <output name="output_rbhb" file="output_paralogous_pairs.tabular" ftype="tabular"/> 202 <output name="output_rbhb" file="output_paralogous_pairs.tabular" ftype="tabular"/>
209 <output name="output_kaks" file="output1.tabular" ftype="tabular"/> 203 <output name="output_kaks" file="output1.tabular" ftype="tabular"/>
210 </test> 204 </test>
211 </tests> 205 </tests>
212 <help> 206 <help>