Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 51:3b2d35b75268 draft

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Uploaded
author greg
date Wed, 08 Feb 2017 14:25:16 -0500
parents a3b7f34ad3f7
children 921804e9ec8c
comparison
equal deleted inserted replaced
50:a3b7f34ad3f7 51:3b2d35b75268
17 #set scaffold_path = $scaffold.fields.path 17 #set scaffold_path = $scaffold.fields.path
18 #set scaffold_dir = $os.path.split($scaffold_path)[0] 18 #set scaffold_dir = $os.path.split($scaffold_path)[0]
19 #set scaffold_selection = $os.path.split($scaffold_path)[1] 19 #set scaffold_selection = $os.path.split($scaffold_path)[1]
20 20
21 #if str($options_type.options_type_selector) == 'advanced': 21 #if str($options_type.options_type_selector) == 'advanced':
22 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
23 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
22 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 24 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
23 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 25 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
24 #set specify_single_copy_cond = $options_type.specify_single_copy_cond 26 #set specify_single_copy_cond = $options_type.specify_single_copy_cond
25 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy 27 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy
28
29 #if str($specify_super_orthogroups) == 'yes':
30 #set specify_super_orthos = True
31 #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups
32 #else:
33 #set specify_super_orthos = False
34 #end if
26 35
27 #if str($specify_single_copy) == 'yes': 36 #if str($specify_single_copy) == 'yes':
28 #set single_copy_orthogroup = True 37 #set single_copy_orthogroup = True
29 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta') 38 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
30 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path 39 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
66 --method $method 75 --method $method
67 --classifier $save_hmmscan_log_cond.classifier 76 --classifier $save_hmmscan_log_cond.classifier
68 --num_threads \${GALAXY_SLOTS:-4} 77 --num_threads \${GALAXY_SLOTS:-4}
69 78
70 #if str($options_type.options_type_selector) == 'advanced': 79 #if str($options_type.options_type_selector) == 'advanced':
71 --super_orthogroups $options_type.super_orthogroups 80 #if specify_super_orthos:
81 --super_orthogroups $super_orthogroups
82 #end if
72 #if $single_copy_orthogroup: 83 #if $single_copy_orthogroup:
73 --single_copy_taxa $single_copy_cond.single_copy_taxa 84 --single_copy_taxa $single_copy_cond.single_copy_taxa
74 --taxa_present $single_copy_cond.taxa_present 85 --taxa_present $single_copy_cond.taxa_present
75 #end if 86 #end if
76 #if str($create_orthogroup) == 'yes': 87 #if str($create_orthogroup) == 'yes':
145 <option value="basic" selected="true">Basic</option> 156 <option value="basic" selected="true">Basic</option>
146 <option value="advanced">Advanced</option> 157 <option value="advanced">Advanced</option>
147 </param> 158 </param>
148 <when value="basic" /> 159 <when value="basic" />
149 <when value="advanced"> 160 <when value="advanced">
150 <param name="super_orthogroups" type="select" label="Super Orthogroups" help="Secondary MCL clusters of orthogroups"> 161 <conditional name="specify_super_orthogroups_cond">
151 <option value="min_evalue" selected="true">Minimum e-value</option> 162 <param name="specify_super_orthogroups" type="select" label="Specify super orthogroups?" help="Secondary MCL clusters of orthogroups">
152 <option value="avg_evalue">Average e-value</option> 163 <option value="no" selected="true">No</option>
153 </param> 164 <option value="yes">Yes</option>
165 </param>
166 <when value="no"/>
167 <when value="yes">
168 <param name="super_orthogroups" type="select" label="Super Orthogroups">
169 <option value="min_evalue" selected="true">Minimum e-value</option>
170 <option value="avg_evalue">Average e-value</option>
171 </param>
172 </when>
173 </conditional>
154 <conditional name="specify_single_copy_cond"> 174 <conditional name="specify_single_copy_cond">
155 <param name="specify_single_copy" type="select" label="Specify single copy orthogroup selection?"> 175 <param name="specify_single_copy" type="select" label="Specify single copy orthogroup selection?">
156 <option value="no" selected="true">No</option> 176 <option value="no" selected="true">No</option>
157 <option value="yes">Yes</option> 177 <option value="yes">Yes</option>
158 </param> 178 </param>