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comparison phylogenomics_analysis.xml @ 5:26f5584ab88a draft

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author greg
date Thu, 05 Jan 2017 09:23:12 -0500
parents 37b56c1befaa
children 21298684d201
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4:37b56c1befaa 5:26f5584ab88a
19 PhylogenomicsAnalysis 19 PhylogenomicsAnalysis
20 --orthogroup_faa "$orthogroup_fna.extra_files_path" 20 --orthogroup_faa "$orthogroup_fna.extra_files_path"
21 --scaffold "$scaffold" 21 --scaffold "$scaffold"
22 --method $method 22 --method $method
23 #if str($options_type.options_type_selector) == 'advanced': 23 #if str($options_type.options_type_selector) == 'advanced':
24 #if str($options_type.multiple_sequence_alignments_cond) == 'yes': 24 #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
25 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
26 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
25 #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond 27 #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
26 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 28 #set multiple_codon_alignments = multiple_codon_alignments_cond.multiple_codon_alignments
27 #if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'create_alignments': 29 #if str($multiple_sequence_alignments_option) == 'create_alignments':
28 --create_alignments 30 --create_alignments
29 #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'add_alignments': 31 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
30 --add_alignments 32 --add_alignments
31 #else if str($multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments': 33 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
32 --pasta_alignments 34 --pasta_alignments
33 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 35 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
34 #end if 36 #end if
35 #if str($multiple_codon_alignments_cond.multiple_codon_alignments) == 'yes': 37 #if str($multiple_codon_alignments) == 'yes':
36 --codon_alignments 38 --codon_alignments
37 --orthogroup_fna "$orthogroup_fna" 39 --orthogroup_fna "$orthogroup_fna"
38 --sequence_type $multiple_codon_alignments_cond.sequence_type 40 --sequence_type $multiple_codon_alignments_cond.sequence_type
39 #end if 41 #end if
40 #end if 42 #end if
87 <option value="advanced">Advanced</option> 89 <option value="advanced">Advanced</option>
88 </param> 90 </param>
89 <when value="basic" /> 91 <when value="basic" />
90 <when value="advanced"> 92 <when value="advanced">
91 <conditional name="multiple_sequence_alignments_cond"> 93 <conditional name="multiple_sequence_alignments_cond">
92 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignemnts options?"> 94 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
93 <option value="no" selected="true">No</option> 95 <option value="no" selected="true">No</option>
94 <option value="yes">Yes</option> 96 <option value="yes">Yes</option>
95 </param> 97 </param>
96 <when value="no" /> 98 <when value="no" />
97 <when value="yes"> 99 <when value="yes">