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comparison kaks_analysis.xml @ 42:ec47f2f694e7 draft

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author greg
date Mon, 23 Oct 2017 13:56:14 -0400
parents 1938f0ed6279
children 174a0fdda6bd
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41:1938f0ed6279 42:ec47f2f694e7
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 = $comparison_cond.blast_option
40 #if str($blast_option) == 'crbblast':
41 --crb_blast
42 #end if
39 #end if 43 #end if
40 #if str($options_type.options_type_selector) == 'advanced': 44 #if str($options_type.options_type_selector) == 'advanced':
41 #if str($set_min_coverage) == 'yes': 45 #if str($set_min_coverage) == 'yes':
42 --min_coverage $set_min_coverage_cond.min_coverage 46 --min_coverage $set_min_coverage_cond.min_coverage
43 #end if 47 #end if
87 </param> 91 </param>
88 <when value="paralogs" /> 92 <when value="paralogs" />
89 <when value="orthologs"> 93 <when value="orthologs">
90 <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" />
91 <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>
92 </when> 100 </when>
93 </conditional> 101 </conditional>
94 <conditional name="options_type"> 102 <conditional name="options_type">
95 <param name="options_type_selector" type="select" label="Options Configuration"> 103 <param name="options_type_selector" type="select" label="Options Configuration">
96 <option value="basic" selected="true">Basic</option> 104 <option value="basic" selected="true">Basic</option>
218 226
219 * **Other options** 227 * **Other options**
220 228
221 - **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. 229 - **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.
222 - **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. 230 - **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.
231
232 - **Determine for cross-species orthologs using** - select option for blast orthology.
233
234 - **reciprocal best BLAST** - use the default stringent reciprocal BLAST package for orthology assignment.
235 - **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.
236
223 - **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. 237 - **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.
224 238
225 - **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. 239 - **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.
226 240
227 - **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. 241 - **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.