Mercurial > repos > greg > kaks_analysis

comparison kaks_analysis.xml @ 4:7fc692c81c02 draft

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Uploaded
author greg
date Wed, 01 Mar 2017 11:16:57 -0500
parents bbc153dbaee7
children a0c58fecc07b
comparison
equal deleted inserted replaced
3:bbc153dbaee7 4:7fc692c81c02
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #set comparison = $comparison_cond.comparison
16 #if str($options_type.options_type_selector) == 'advanced': 17 #if str($options_type.options_type_selector) == 'advanced':
17 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond 18 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
18 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select 19 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
19 #set fit_components_cond = $options_type.fit_components_cond 20 #set fit_components_cond = $options_type.fit_components_cond
20 #set fit_components = $fit_components_cond.fit_components 21 #set fit_components = $fit_components_cond.fit_components
23 --config_dir '$scaffold.fields.path' 24 --config_dir '$scaffold.fields.path'
24 --num_threads \${GALAXY_SLOTS:-4} 25 --num_threads \${GALAXY_SLOTS:-4}
25 --coding_sequences_species_1 '$coding_sequences_species_1' 26 --coding_sequences_species_1 '$coding_sequences_species_1'
26 --proteins_species_1 '$proteins_species_1' 27 --proteins_species_1 '$proteins_species_1'
27 --comparison $comparison 28 --comparison $comparison
28 #if str($comparison_cond.comparison) == 'orthologs': 29 #if str($comparison) == 'orthologs':
29 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2' 30 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
30 --proteins_species_2 '$comparison_cond.proteins_species_2' 31 --proteins_species_2 '$comparison_cond.proteins_species_2'
31 #end if 32 #end if
32 #if str($options_type.options_type_selector) == 'advanced': 33 #if str($options_type.options_type_selector) == 'advanced':
33 --min_coverage $min_coverage 34 --min_coverage $min_coverage