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comparison kaks_analysis.xml @ 16:f5f97d8c4207 draft

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author greg
date Thu, 02 Mar 2017 10:23:21 -0500
parents 01278db07d6f
children af3fa1382322
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15:01278db07d6f 16:f5f97d8c4207
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 23 #set recalibrate_cond = $options_type.recalibrate_cond
24 #set recalibrate = $recalibrate_cond.recalibrate 24 #set recalibrate = $recalibrate_cond.recalibrate
25 #set set_min_coverage_cond = $options_type.set_min_coverage_cond 25 #set set_min_coverage_cond = $options_type.set_min_coverage_cond
26 #set set_min_coverage = $set_min_coverage_cond.set_min_coverage 26 #set set_min_coverage = $set_min_coverage_cond.set_min_coverage
27 #set set_lower_ks_limit_cond = $options_cond.set_lower_ks_limit_cond
28 #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit
29 #set set_upper_ks_limit_cond = $options_cond.set_upper_ks_limit_cond
30 #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit
27 #else: 31 #else:
28 #set codeml_ctl_file_select = 'no' 32 #set codeml_ctl_file_select = 'no'
29 #set fit_components = 'no' 33 #set fit_components = 'no'
34 #set set_lower_ks_limit = 'no'
35 #set set_upper_ks_limit = 'no'
30 #end if 36 #end if
31 KaKsAnalysis 37 KaKsAnalysis
32 --config_dir '$scaffold.fields.path' 38 --config_dir '$scaffold.fields.path'
33 --num_threads \${GALAXY_SLOTS:-4} 39 --num_threads \${GALAXY_SLOTS:-4}
34 --coding_sequences_species_1 '$coding_sequences_species_1' 40 --coding_sequences_species_1 '$coding_sequences_species_1'
51 # will be used if the --codeml_ctl_file flag is missing. 57 # will be used if the --codeml_ctl_file flag is missing.
52 #end if 58 #end if
53 #if str($fit_components) == 'yes': 59 #if str($fit_components) == 'yes':
54 --fit_components 60 --fit_components
55 --num_of_components $fit_components_cond.num_of_components 61 --num_of_components $fit_components_cond.num_of_components
56 --min_ks $fit_components_cond.min_ks 62 #end if
57 --max_ks $fit_components_cond.max_ks 63 #if str($set_lower_ks_limit) == 'yes':
64 --min_ks $set_lower_ks_limit_cond.min_ks
65 #end if
66 #if str($set_upper_ks_limit) == 'yes':
67 --max_ks $set_upper_ks_limit_cond.max_ks
58 #end if 68 #end if
59 #end if 69 #end if
60 >/dev/null 70 >/dev/null
61 && mv $output_dir/species1.fna '$output_species1_fna' 71 && mv $output_dir/species1.fna '$output_species1_fna'
62 && mv $output_dir/species1.faa '$output_species1_faa' 72 && mv $output_dir/species1.faa '$output_species1_faa'
136 <option value="yes">Yes</option> 146 <option value="yes">Yes</option>
137 </param> 147 </param>
138 <when value="no" /> 148 <when value="no" />
139 <when value="yes"> 149 <when value="yes">
140 <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" /> 150 <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" />
141 <param name="min_ks" type="float" value="0.0" min="0.0" label="Lower limit of synonymous subsitutions (ks)" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome" /> 151 </when>
142 <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" help="Excludes likey ancient paralogous pairs" /> 152 </conditional>
153 <conditional name="set_lower_ks_limit_cond">
154 <param name="set_lower_ks_limit" type="select" label="Set lower limit of synonymous subsitutions (ks)?" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome">
155 <option value="no" selected="true">No</option>
156 <option value="yes">Yes</option>
157 </param>
158 <when value="no" />
159 <when value="yes">
160 <param name="min_ks" type="float" value="0.0" min="0.0" label="Lower limit of synonymous subsitutions (ks)" />
161 </when>
162 </conditional>
163 <conditional name="set_upper_ks_limit_cond">
164 <param name="set_upper_ks_limit" type="select" label="Set upper limit of synonymous subsitutions (ks)?" help="Excludes likey ancient paralogous pairs">
165 <option value="no" selected="true">No</option>
166 <option value="yes">Yes</option>
167 </param>
168 <when value="no" />
169 <when value="yes">
170 <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" />
143 </when> 171 </when>
144 </conditional> 172 </conditional>
145 </when> 173 </when>
146 </conditional> 174 </conditional>
147 <!-- Required due to the Emmix license --> 175 <!-- Required due to the Emmix license -->