Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 67:062883e3392c draft

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author greg
date Mon, 13 Feb 2017 09:11:32 -0500
parents 7525307aa1d7
children 8342ceb01855
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66:7525307aa1d7 67:062883e3392c
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #import os 16 #import os
17 #set scaffold_path = $scaffold.fields.path
18 #set scaffold_dir = $os.path.split($scaffold_path)[0]
19 #set scaffold_selection = $os.path.split($scaffold_path)[1]
20 17
21 #if str($options_type.options_type_selector) == 'advanced': 18 #if str($options_type.options_type_selector) == 'advanced':
22 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond 19 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
23 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups 20 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
24 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 21 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
71 #set create_corresponding_coding_sequences = False 68 #set create_corresponding_coding_sequences = False
72 #end if 69 #end if
73 70
74 GeneFamilyClassifier 71 GeneFamilyClassifier
75 --proteins '$input' 72 --proteins '$input'
76 --scaffold_dir '$scaffold_dir' 73 --scaffold '$scaffold.fields.path'
77 --scaffold '$scaffold_selection'
78 --method $method 74 --method $method
79 --classifier $save_hmmscan_log_cond.classifier 75 --classifier $save_hmmscan_log_cond.classifier
80 --num_threads \${GALAXY_SLOTS:-4} 76 --num_threads \${GALAXY_SLOTS:-4}
81 77
82 #if str($options_type.options_type_selector) == 'advanced': 78 #if str($options_type.options_type_selector) == 'advanced':
276 272
277 ----- 273 -----
278 274
279 **Options** 275 **Options**
280 276
281 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 277 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
282 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 278 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
283 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive). 279 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
284 * **Super Orthogroups** - Secondary MCL clusters of orthogroups. 280 * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
285 * **Specify single copy orthogroup selection?** - Select 'Yes' to specify 'Minimum single copy taxa required in orthogroup'. 281 * **Specify single copy orthogroup selection?** - Select 'Yes' to specify 'Minimum single copy taxa required in orthogroup'.
286 * **Minimum single copy taxa required in orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only. 282 * **Minimum single copy taxa required in orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.