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comparison kaks_analysis.xml @ 11:a0b1f599becc draft

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author greg
date Wed, 01 Mar 2017 14:17:43 -0500
parents f8558fb37545
children 7945134d3956
comparison
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10:f8558fb37545 11:a0b1f599becc
18 #if str($options_type.options_type_selector) == 'advanced': 18 #if str($options_type.options_type_selector) == 'advanced':
19 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond 19 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
20 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select 20 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
21 #set fit_components_cond = $options_type.fit_components_cond 21 #set fit_components_cond = $options_type.fit_components_cond
22 #set fit_components = $fit_components_cond.fit_components 22 #set fit_components = $fit_components_cond.fit_components
23 #set recalibrate_cond = $options_type.recalibrate_cond
24 #set recalibrate = $recalibrate_cond.recalibrate
25 #set set_min_coverage_cond = $options_type.set_min_coverage_cond
26 #set set_min_coverage = $set_min_coverage_cond.set_min_coverage
23 #else: 27 #else:
24 #set codeml_ctl_file_select = 'no' 28 #set codeml_ctl_file_select = 'no'
25 #set fit_components = 'no' 29 #set fit_components = 'no'
26 #end if 30 #end if
27 KaKsAnalysis 31 KaKsAnalysis
33 #if str($comparison) == 'orthologs': 37 #if str($comparison) == 'orthologs':
34 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2' 38 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
35 --proteins_species_2 '$comparison_cond.proteins_species_2' 39 --proteins_species_2 '$comparison_cond.proteins_species_2'
36 #end if 40 #end if
37 #if str($options_type.options_type_selector) == 'advanced': 41 #if str($options_type.options_type_selector) == 'advanced':
38 --min_coverage $options_type.min_coverage 42 #if str($set_min_coverage) == 'yes':
39 --recalibration_rate $options_type.recalibration_rate 43 --min_coverage $set_min_coverage_cond.min_coverage
44 #end if
45 #if str($recalibrate) == 'yes':
46 --recalibration_rate $recalibrate_cond.recalibration_rate
47 #end if
40 #if str($codeml_ctl_file_select) == 'yes': 48 #if str($codeml_ctl_file_select) == 'yes':
41 --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file' 49 --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file'
42 # No else block needed here because the default codeml_ctl config 50 # No else block needed here because the default codeml_ctl config
43 # will be used if the --codeml_ctl_file flag is missing. 51 # will be used if the --codeml_ctl_file flag is missing.
44 #end if 52 #end if
90 <option value="basic" selected="true">Basic</option> 98 <option value="basic" selected="true">Basic</option>
91 <option value="advanced">Advanced</option> 99 <option value="advanced">Advanced</option>
92 </param> 100 </param>
93 <when value="basic" /> 101 <when value="basic" />
94 <when value="advanced"> 102 <when value="advanced">
95 <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum sequence pairwise coverage length between homologous pairs" /> 103 <conditional name="set_min_coverage_cond">
96 <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Predetermined evolutionary rate for recalibrating synonymous subsitutions (ks) of species" /> 104 <param name="set_min_coverage" type="select" label="Specify minimum sequence pairwise coverage length between homologous pairs?">
105 <option value="no" selected="true">No</option>
106 <option value="yes">Yes</option>
107 </param>
108 <when value="no" />
109 <when value="yes">
110 <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum sequence pairwise coverage length between homologous pairs" />
111 </when>
112 </conditional>
113 <conditional name="recalibrate_cond">
114 <param name="recalibrate" type="select" label="Specify evolutionary rate for recalibrating synonymous subsitutions (ks) of species?">
115 <option value="no" selected="true">No</option>
116 <option value="yes">Yes</option>
117 </param>
118 <when value="no" />
119 <when value="yes">
120 <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Evolutionary rate for recalibrating synonymous subsitutions (ks) of species" />
121 </when>
122 </conditional>
97 <conditional name="codeml_ctl_file_cond"> 123 <conditional name="codeml_ctl_file_cond">
98 <param name="codeml_ctl_file_select" type="select" label="Select PAML codeml control file?" help="Used for ML analysis of protein-coding DNA sequences using codon substitution models, select No to use the default control file"> 124 <param name="codeml_ctl_file_select" type="select" label="Select PAML codeml control file?" help="Used for ML analysis of protein-coding DNA sequences using codon substitution models, select No to use the default control file">
99 <option value="no" selected="true">No</option> 125 <option value="no" selected="true">No</option>
100 <option value="yes">Yes</option> 126 <option value="yes">Yes</option>
101 </param> 127 </param>