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comparison kaks_analysis.xml @ 37:b7a3dce9c4f7 draft

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author greg
date Thu, 08 Jun 2017 10:25:44 -0400
parents ff040a476523
children 508a2dcfc943
comparison
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36:ff040a476523 37:b7a3dce9c4f7
2 <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description> 2 <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_kaks_analysis" /> 6 <expand macro="requirements_kaks_analysis" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 #set output_dir = 'kaksAnalysis_dir'
9 #set output_dir = 'kaksAnalysis_dir' 9 #set comparison = $comparison_cond.comparison
10 #set comparison = $comparison_cond.comparison 10 #if str($options_type.options_type_selector) == 'advanced':
11 #if str($options_type.options_type_selector) == 'advanced': 11 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
12 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond 12 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
13 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select 13 #set fit_components_cond = $options_type.fit_components_cond
14 #set fit_components_cond = $options_type.fit_components_cond 14 #set fit_components = $fit_components_cond.fit_components
15 #set fit_components = $fit_components_cond.fit_components 15 #set recalibrate_cond = $options_type.recalibrate_cond
16 #set recalibrate_cond = $options_type.recalibrate_cond 16 #set recalibrate = $recalibrate_cond.recalibrate
17 #set recalibrate = $recalibrate_cond.recalibrate 17 #set set_min_coverage_cond = $options_type.set_min_coverage_cond
18 #set set_min_coverage_cond = $options_type.set_min_coverage_cond 18 #set set_min_coverage = $set_min_coverage_cond.set_min_coverage
19 #set set_min_coverage = $set_min_coverage_cond.set_min_coverage 19 #set set_lower_ks_limit_cond = $options_type.set_lower_ks_limit_cond
20 #set set_lower_ks_limit_cond = $options_type.set_lower_ks_limit_cond 20 #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit
21 #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit 21 #set set_upper_ks_limit_cond = $options_type.set_upper_ks_limit_cond
22 #set set_upper_ks_limit_cond = $options_type.set_upper_ks_limit_cond 22 #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit
23 #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit 23 #else:
24 #else: 24 #set codeml_ctl_file_select = 'no'
25 #set codeml_ctl_file_select = 'no' 25 #set fit_components = 'no'
26 #set fit_components = 'no' 26 #set set_lower_ks_limit = 'no'
27 #set set_lower_ks_limit = 'no' 27 #set set_upper_ks_limit = 'no'
28 #set set_upper_ks_limit = 'no' 28 #end if
29 #end if 29 KaKsAnalysis
30 KaKsAnalysis 30 --num_threads \${GALAXY_SLOTS:-4}
31 --num_threads \${GALAXY_SLOTS:-4} 31 --coding_sequences_species_1 '$coding_sequences_species_1'
32 --coding_sequences_species_1 '$coding_sequences_species_1' 32 --proteins_species_1 '$proteins_species_1'
33 --proteins_species_1 '$proteins_species_1' 33 --comparison $comparison
34 --comparison $comparison 34 #if str($comparison) == 'orthologs':
35 #if str($comparison) == 'orthologs': 35 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
36 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2' 36 --proteins_species_2 '$comparison_cond.proteins_species_2'
37 --proteins_species_2 '$comparison_cond.proteins_species_2' 37 #end if
38 #end if 38 #if str($options_type.options_type_selector) == 'advanced':
39 #if str($options_type.options_type_selector) == 'advanced': 39 #if str($set_min_coverage) == 'yes':
40 #if str($set_min_coverage) == 'yes': 40 --min_coverage $set_min_coverage_cond.min_coverage
41 --min_coverage $set_min_coverage_cond.min_coverage 41 #end if
42 #end if 42 #if str($recalibrate) == 'yes':
43 #if str($recalibrate) == 'yes': 43 --recalibration_rate $recalibrate_cond.recalibration_rate
44 --recalibration_rate $recalibrate_cond.recalibration_rate 44 #end if
45 #end if 45 #if str($codeml_ctl_file_select) == 'yes':
46 #if str($codeml_ctl_file_select) == 'yes': 46 --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file'
47 --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file' 47 # No else block needed here because the default codeml_ctl config
48 # No else block needed here because the default codeml_ctl config 48 # will be used if the --codeml_ctl_file flag is missing.
49 # will be used if the --codeml_ctl_file flag is missing. 49 #end if
50 #end if 50 #if str($fit_components) == 'yes':
51 #if str($fit_components) == 'yes': 51 --fit_components
52 --fit_components 52 --num_of_components $fit_components_cond.num_of_components
53 --num_of_components $fit_components_cond.num_of_components 53 #end if
54 #end if 54 #if str($set_lower_ks_limit) == 'yes':
55 #if str($set_lower_ks_limit) == 'yes': 55 --min_ks $set_lower_ks_limit_cond.min_ks
56 --min_ks $set_lower_ks_limit_cond.min_ks 56 #end if
57 #end if 57 #if str($set_upper_ks_limit) == 'yes':
58 #if str($set_upper_ks_limit) == 'yes': 58 --max_ks $set_upper_ks_limit_cond.max_ks
59 --max_ks $set_upper_ks_limit_cond.max_ks 59 #end if
60 #end if 60 #end if
61 #end if 61 >/dev/null
62 >/dev/null 62 && mv $output_dir/species1.fna '$output_species1_fna'
63 && mv $output_dir/species1.fna '$output_species1_fna' 63 && mv $output_dir/species1.faa '$output_species1_faa'
64 && mv $output_dir/species1.faa '$output_species1_faa' 64 #if str($comparison) == 'paralogs':
65 #if str($comparison) == 'paralogs': 65 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
66 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' 66 #else:
67 #else: 67 && mv $output_dir/species2.faa '$output_species2_faa'
68 && mv $output_dir/species2.faa '$output_species2_faa' 68 && mv $output_dir/species2.fna '$output_species2_fna'
69 && mv $output_dir/species2.fna '$output_species2_fna' 69 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
70 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' 70 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
71 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' 71 #end if
72 #end if 72 && mv $output_dir/*.rbhb '$output_rbhb'
73 && mv $output_dir/*.rbhb '$output_rbhb' 73 && mv $output_dir/*.kaks '$output_kaks'
74 && mv $output_dir/*.kaks '$output_kaks' 74 #if str($fit_components) == 'yes':
75 #if str($fit_components) == 'yes': 75 && mv $output_dir/*.components '$output_components'
76 && mv $output_dir/*.components '$output_components' 76 #end if
77 #end if 77 ]]></command>
78 ]]>
79 </command>
80 <inputs> 78 <inputs>
81 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" /> 79 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" />
82 <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" /> 80 <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" />
83 <conditional name="comparison_cond"> 81 <conditional name="comparison_cond">
84 <param name="comparison" type="select" label="Type of sequence comparison"> 82 <param name="comparison" type="select" label="Type of sequence comparison">