Mercurial > repos > greg > plant_tribes_kaks_analysis
comparison kaks_analysis.xml @ 4:48271ee78198 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 21 Dec 2017 09:17:01 -0500 |
| parents | 1fb0f2092177 |
| children | a5639484fb63 |
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| 3:1fb0f2092177 | 4:48271ee78198 |
|---|---|
| 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"> |