Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 68:8342ceb01855 draft

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Uploaded
author greg
date Wed, 15 Feb 2017 11:16:24 -0500
parents 062883e3392c
children 0d689b9662ec
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67:062883e3392c 68:8342ceb01855
49 #end if 49 #end if
50 50
51 #if str($specify_single_copy) == 'yes': 51 #if str($specify_single_copy) == 'yes':
52 #set single_copy_orthogroup = True 52 #set single_copy_orthogroup = True
53 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond 53 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
54 ## FixMe: the single_copy_custom option is not currently supported.
55 #set single_copy = $single_copy_cond.single_copy 54 #set single_copy = $single_copy_cond.single_copy
56 #if $create_ortho_sequences: 55 #if $create_ortho_sequences:
57 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta') 56 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
58 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path 57 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
59 mkdir -p $single_copy_fasta_dest_dir && 58 mkdir -p $single_copy_fasta_dest_dir &&
71 GeneFamilyClassifier 70 GeneFamilyClassifier
72 --proteins '$input' 71 --proteins '$input'
73 --scaffold '$scaffold.fields.path' 72 --scaffold '$scaffold.fields.path'
74 --method $method 73 --method $method
75 --classifier $save_hmmscan_log_cond.classifier 74 --classifier $save_hmmscan_log_cond.classifier
75 --config_dir '$scaffold.fields.config_path'
76 --num_threads \${GALAXY_SLOTS:-4} 76 --num_threads \${GALAXY_SLOTS:-4}
77 77
78 #if str($options_type.options_type_selector) == 'advanced': 78 #if str($options_type.options_type_selector) == 'advanced':
79 #if specify_super_orthos: 79 #if specify_super_orthos:
80 --super_orthogroups $super_orthogroups 80 --super_orthogroups $super_orthogroups
81 #end if 81 #end if
82 #if $single_copy_orthogroup: 82 #if $single_copy_orthogroup:
83 --single_copy_taxa $single_copy_cond.single_copy_taxa 83 #if str($single_copy) == 'custom':
84 --taxa_present $single_copy_cond.taxa_present 84 --single_copy_custom
85 #else:
86 --single_copy_taxa $single_copy_cond.single_copy_taxa
87 --taxa_present $single_copy_cond.taxa_present
88 #end if
85 #end if 89 #end if
86 #if str($create_orthogroup) == 'yes': 90 #if str($create_orthogroup) == 'yes':
87 --orthogroup_fasta 91 --orthogroup_fasta
88 #if $create_corresponding_coding_sequences: 92 #if $create_corresponding_coding_sequences:
89 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences' 93 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
178 </param> 182 </param>
179 <when value="no"/> 183 <when value="no"/>
180 <when value="yes"> 184 <when value="yes">
181 <conditional name="single_copy_cond"> 185 <conditional name="single_copy_cond">
182 <param name="single_copy" type="select" label="Select single copy configuration"> 186 <param name="single_copy" type="select" label="Select single copy configuration">
183 <!-- 187 <option value="custom" selected="true">Single copy orthogroup custom configuration</option>
184 FixMe: single_copy_custom is not currently supported because the
185 ~/config/*.singleCopy.config files are not easy to manage by a suer
186 and the GeneFamilyClassifier pipeline must be enhanced to provide an
187 optional parameter for the hard-coded path to the config.
188 <option value="custom" selected="true">Single copy orthogroup custom</option>
189 -->
190 <option value="taxa">Minimum single copy taxa required in orthogroup</option> 188 <option value="taxa">Minimum single copy taxa required in orthogroup</option>
191 </param> 189 </param>
192 <when value="custom" /> 190 <when value="custom"/>
193 <when value="taxa"> 191 <when value="taxa">
194 <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/> 192 <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/>
195 <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/> 193 <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/>
196 </when> 194 </when>
197 </conditional> 195 </conditional>