Mercurial > repos > greg > plant_tribes_kaks_analysis

comparison kaks_analysis.xml @ 5:a5639484fb63 draft

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Uploaded
author greg
date Mon, 22 Jan 2018 13:32:39 -0500
parents 48271ee78198
children 2c46551274d6
comparison
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4:48271ee78198 5:a5639484fb63
77 cp kaks_analysis_log.txt '$output_species2_ortholog'; 77 cp kaks_analysis_log.txt '$output_species2_ortholog';
78 cp kaks_analysis_log.txt '$output_rbhb_ortholog'; 78 cp kaks_analysis_log.txt '$output_rbhb_ortholog';
79 #end if 79 #end if
80 cp kaks_analysis_log.txt '$output_kaks'; 80 cp kaks_analysis_log.txt '$output_kaks';
81 #if str($fit_components) == 'yes': 81 #if str($fit_components) == 'yes':
82 cp kaks_analysis_log.txt '$output_components' 82 cp kaks_analysis_log.txt '$output_components';
83 #end if 83 #end if
84 else 84 else
85 && mv $output_dir/species1.fna '$output_species1_fna' 85 mv $output_dir/species1.fna '$output_species1_fna';
86 && mv $output_dir/species1.faa '$output_species1_faa' 86 mv $output_dir/species1.faa '$output_species1_faa';
87 #if str($comparison) == 'paralogs': 87 #if str($comparison) == 'paralogs':
88 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' 88 mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog';
89 && mv $output_dir/*.rbhb '$output_rbhb_paralog' 89 mv $output_dir/*.rbhb '$output_rbhb_paralog';
90 #else: 90 #else:
91 && mv $output_dir/species2.faa '$output_species2_faa' 91 mv $output_dir/species2.faa '$output_species2_faa';
92 && mv $output_dir/species2.fna '$output_species2_fna' 92 mv $output_dir/species2.fna '$output_species2_fna';
93 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' 93 mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog';
94 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' 94 mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog';
95 && mv $output_dir/*.rbhb '$output_rbhb_ortholog' 95 mv $output_dir/*.rbhb '$output_rbhb_ortholog';
96 #end if 96 #end if
97 && mv $output_dir/*.kaks '$output_kaks' 97 mv $output_dir/*.kaks '$output_kaks';
98 #if str($fit_components) == 'yes': 98 #if str($fit_components) == 'yes':
99 && mv $output_dir/*.components '$output_components' 99 mv $output_dir/*.components '$output_components';
100 #end if 100 #end if
101 fi 101 fi
102 ]]></command> 102 ]]></command>
103 <inputs> 103 <inputs>
104 <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" />