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comparison kaks_analysis.xml @ 3:1fb0f2092177 draft

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author greg
date Mon, 30 Oct 2017 09:54:20 -0400
parents 2fe7044626ac
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2:2fe7044626ac 3:1fb0f2092177
1 <tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="@WRAPPER_VERSION@.2"> 1 <tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="@WRAPPER_VERSION@.3.0">
2 <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description> 2 <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_kaks_analysis" /> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_kaks_analysis</requirement>
8 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #set output_dir = 'kaksAnalysis_dir' 10 #set output_dir = 'kaksAnalysis_dir'
9 #set comparison = $comparison_cond.comparison 11 #set comparison = $comparison_cond.comparison
10 #if str($options_type.options_type_selector) == 'advanced': 12 #if str($options_type.options_type_selector) == 'advanced':
11 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond 13 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
32 --proteins_species_1 '$proteins_species_1' 34 --proteins_species_1 '$proteins_species_1'
33 --comparison $comparison 35 --comparison $comparison
34 #if str($comparison) == 'orthologs': 36 #if str($comparison) == 'orthologs':
35 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2' 37 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
36 --proteins_species_2 '$comparison_cond.proteins_species_2' 38 --proteins_species_2 '$comparison_cond.proteins_species_2'
39 #if str($comparison_cond.blast_option) == 'crbblast':
40 --crb_blast
41 #end if
37 #end if 42 #end if
38 #if str($options_type.options_type_selector) == 'advanced': 43 #if str($options_type.options_type_selector) == 'advanced':
39 #if str($set_min_coverage) == 'yes': 44 #if str($set_min_coverage) == 'yes':
40 --min_coverage $set_min_coverage_cond.min_coverage 45 --min_coverage $set_min_coverage_cond.min_coverage
41 #end if 46 #end if
56 #end if 61 #end if
57 #if str($set_upper_ks_limit) == 'yes': 62 #if str($set_upper_ks_limit) == 'yes':
58 --max_ks $set_upper_ks_limit_cond.max_ks 63 --max_ks $set_upper_ks_limit_cond.max_ks
59 #end if 64 #end if
60 #end if 65 #end if
61 >/dev/null 66 &>proc.log
62 && mv $output_dir/species1.fna '$output_species1_fna' 67 && mv $output_dir/species1.fna '$output_species1_fna'
63 && mv $output_dir/species1.faa '$output_species1_faa' 68 && mv $output_dir/species1.faa '$output_species1_faa'
64 #if str($comparison) == 'paralogs': 69 #if str($comparison) == 'paralogs':
65 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' 70 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
71 && mv $output_dir/*.rbhb '$output_rbhb_paralog'
66 #else: 72 #else:
67 && mv $output_dir/species2.faa '$output_species2_faa' 73 && mv $output_dir/species2.faa '$output_species2_faa'
68 && mv $output_dir/species2.fna '$output_species2_fna' 74 && mv $output_dir/species2.fna '$output_species2_fna'
69 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' 75 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
70 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' 76 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
71 #end if 77 && mv $output_dir/*.rbhb '$output_rbhb_ortholog'
72 && mv $output_dir/*.rbhb '$output_rbhb' 78 #end if
73 && mv $output_dir/*.kaks '$output_kaks' 79 && mv $output_dir/*.kaks '$output_kaks'
74 #if str($fit_components) == 'yes': 80 #if str($fit_components) == 'yes':
75 && mv $output_dir/*.components '$output_components' 81 && mv $output_dir/*.components '$output_components'
76 #end if 82 #end if
77 ]]></command> 83 ]]></command>
85 </param> 91 </param>
86 <when value="paralogs" /> 92 <when value="paralogs" />
87 <when value="orthologs"> 93 <when value="orthologs">
88 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences for the second species" /> 94 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences for the second species" />
89 <param name="proteins_species_2" format="fasta" type="data" label="Protein sequences for the second species" /> 95 <param name="proteins_species_2" format="fasta" type="data" label="Protein sequences for the second species" />
96 <param name="blast_option" type="select" display="radio" label="Determine for cross-species orthologs using">
97 <option value="blast" selected="true">reciprocal best BLAST</option>
98 <option value="crbblast">conditional reciprocal best BLAST</option>
99 </param>
90 </when> 100 </when>
91 </conditional> 101 </conditional>
92 <conditional name="options_type"> 102 <conditional name="options_type">
93 <param name="options_type_selector" type="select" label="Options Configuration"> 103 <param name="options_type_selector" type="select" label="Options Configuration">
94 <option value="basic" selected="true">Basic</option> 104 <option value="basic" selected="true">Basic</option>
162 <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"> 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">
163 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> 173 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
164 </param> 174 </param>
165 </inputs> 175 </inputs>
166 <outputs> 176 <outputs>
167 <data name="output_species1_fna" format="fasta" label="${tool.name} (coding sequences) on ${on_string}" /> 177 <data name="output_species1_fna" format="fasta" label="${tool.name} (coding sequences species1) on ${on_string}" />
168 <data name="output_species1_faa" format="fasta" label="${tool.name} (amino acids) on ${on_string}" /> 178 <data name="output_species1_faa" format="fasta" label="${tool.name} (amino acids species1) on ${on_string}" />
169 <data name="output_species2_fna" format="fasta" label="${tool.name} (coding sequences) on ${on_string}"> 179 <data name="output_species2_fna" format="fasta" label="${tool.name} (coding sequences species2) on ${on_string}">
170 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 180 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
171 </data> 181 </data>
172 <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids) on ${on_string}"> 182 <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids species2) on ${on_string}">
173 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 183 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
174 </data> 184 </data>
175 <data name="output_species1_paralog" format="tabular" label="${tool.name} (blastn results) on ${on_string}"> 185 <data name="output_species1_paralog" format="tabular" label="${tool.name} (blastn results species1 vs species1) on ${on_string}">
176 <filter>comparison_cond['comparison'] == 'paralogs'</filter> 186 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
177 </data> 187 </data>
178 <data name="output_species1_ortholog" format="tabular" label="${tool.name} (blastn results) on ${on_string}"> 188 <data name="output_species1_ortholog" format="tabular" label="${tool.name} (blastn results species1 vs species2) on ${on_string}">
179 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 189 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
180 </data> 190 </data>
181 <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results) on ${on_string}"> 191 <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results species2 vs species1) on ${on_string}">
182 <filter>comparison_cond['comparison'] == 'orthologs'</filter> 192 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
183 </data> 193 </data>
184 <data name="output_rbhb" format="tabular" label="${tool.name} (paralogous pairs) on ${on_string}" /> 194 <data name="output_rbhb_paralog" format="tabular" label="${tool.name} (paralogous pairs) on ${on_string}">
185 <data name="output_kaks" format="tabular" label="${tool.name} on ${on_string}" /> 195 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
186 <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the ks distribution) on ${on_string}"> 196 </data>
197 <data name="output_rbhb_ortholog" format="tabular" label="${tool.name} (orthologous pairs) on ${on_string}">
198 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
199 </data>
200 <data name="output_kaks" format="tabular" label="${tool.name} (KaKs distribution) on ${on_string}" />
201 <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the KaKs distribution) on ${on_string}">
187 <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>
188 </data> 203 </data>
189 </outputs> 204 </outputs>
190 <tests> 205 <tests>
191 <test> 206 <test>
193 <param name="proteins_species_1" value="species1_pep.fasta" ftype="fasta"/> 208 <param name="proteins_species_1" value="species1_pep.fasta" ftype="fasta"/>
194 <param name="non_commercial_use" value="True"/> 209 <param name="non_commercial_use" value="True"/>
195 <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"/>
196 <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"/>
197 <output name="output_species1_paralog" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/> 212 <output name="output_species1_paralog" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/>
198 <output name="output_rbhb" file="output_paralogous_pairs.tabular" ftype="tabular"/> 213 <output name="output_rbhb_paralog" file="output_paralogous_pairs.tabular" ftype="tabular"/>
199 <output name="output_kaks" file="output1.tabular" ftype="tabular"/> 214 <output name="output_kaks" file="output1.tabular" ftype="tabular"/>
200 </test> 215 </test>
201 </tests> 216 </tests>
202 <help> 217 <help>
203 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
216 231
217 * **Other options** 232 * **Other options**
218 233
219 - **Coding sequences for the second species** - coding sequence fasta file for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison. 234 - **Coding sequences for the second species** - coding sequence fasta file for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison.
220 - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison. 235 - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history. This option is required only for orthologous comparison.
236
237 - **Determine for cross-species orthologs using** - select option for blast orthology.
238
239 - **reciprocal best BLAST** - use the default stringent reciprocal BLAST package for orthology assignment.
240 - **conditional reciprocal best BLAST** - use the CRB-BLAST package for orthology assignment which increases sensitivity to orthology comparisons and determines additional cross-species orthologs that are being left out by the defaul stringent reciprocal BLAST.
241
221 - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs. PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage. By default, the match score is set to 0.5 if 'No' is selected. 242 - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs. PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage. By default, the match score is set to 0.5 if 'No' is selected.
222 243
223 - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0. 244 - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0.
224 245
225 - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in [7]. Rate recalibration applies only to paralogous comparisons. 246 - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in [7]. Rate recalibration applies only to paralogous comparisons.