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comparison kaks_analysis.xml @ 52:c6ed6c138b14 draft

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author greg
date Wed, 13 Dec 2017 14:10:46 -0500
parents 57674bef753b
children 283dc861c75c
comparison
equal deleted inserted replaced
51:57674bef753b 52:c6ed6c138b14
61 #end if 61 #end if
62 #if str($set_upper_ks_limit) == 'yes': 62 #if str($set_upper_ks_limit) == 'yes':
63 --max_ks $set_upper_ks_limit_cond.max_ks 63 --max_ks $set_upper_ks_limit_cond.max_ks
64 #end if 64 #end if
65 #end if 65 #end if
66 &>proc.log 66 &>kaks_analysis_log.txt;
67 && mv $output_dir/species1.fna '$output_species1_fna' 67 if [[ $? -ne 0 ]]; then
68 && mv $output_dir/species1.faa '$output_species1_faa' 68 cp kaks_analysis_log.txt '$output_species1_fna';
69 #if str($comparison) == 'paralogs': 69 cp kaks_analysis_log.txt '$output_species1_faa';
70 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' 70 #if str($comparison) == 'paralogs':
71 && mv $output_dir/*.rbhb '$output_rbhb_paralog' 71 cp kaks_analysis_log.txt '$output_species1_paralog';
72 #else: 72 cp kaks_analysis_log.txt '$output_rbhb_paralog';
73 && mv $output_dir/species2.faa '$output_species2_faa' 73 #else:
74 && mv $output_dir/species2.fna '$output_species2_fna' 74 cp kaks_analysis_log.txt '$output_species2_faa';
75 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' 75 cp kaks_analysis_log.txt '$output_species2_fna';
76 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' 76 cp kaks_analysis_log.txt '$output_species1_ortholog';
77 && mv $output_dir/*.rbhb '$output_rbhb_ortholog' 77 cp kaks_analysis_log.txt '$output_species2_ortholog';
78 #end if 78 cp kaks_analysis_log.txt '$output_rbhb_ortholog';
79 && mv $output_dir/*.kaks '$output_kaks' 79 #end if
80 #if str($fit_components) == 'yes': 80 cp kaks_analysis_log.txt '$output_kaks';
81 && mv $output_dir/*.components '$output_components' 81 #if str($fit_components) == 'yes':
82 #end if 82 cp kaks_analysis_log.txt '$output_components'
83 #end if
84 else
85 && mv $output_dir/species1.fna '$output_species1_fna'
86 && mv $output_dir/species1.faa '$output_species1_faa'
87 #if str($comparison) == 'paralogs':
88 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
89 && mv $output_dir/*.rbhb '$output_rbhb_paralog'
90 #else:
91 && mv $output_dir/species2.faa '$output_species2_faa'
92 && mv $output_dir/species2.fna '$output_species2_fna'
93 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
94 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
95 && mv $output_dir/*.rbhb '$output_rbhb_ortholog'
96 #end if
97 && mv $output_dir/*.kaks '$output_kaks'
98 #if str($fit_components) == 'yes':
99 && mv $output_dir/*.components '$output_components'
100 #end if
101 fi
83 ]]></command> 102 ]]></command>
84 <inputs> 103 <inputs>
85 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" /> 104 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" />
86 <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" /> 105 <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" />
87 <conditional name="comparison_cond"> 106 <conditional name="comparison_cond">