Mercurial > repos > greg > plant_tribes_kaks_analysis
changeset 4:48271ee78198 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 21 Dec 2017 09:17:01 -0500 |
| parents | 1fb0f2092177 |
| children | a5639484fb63 |
| files | kaks_analysis.xml |
| diffstat | 1 files changed, 36 insertions(+), 17 deletions(-) [+] |
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--- a/kaks_analysis.xml Mon Oct 30 09:54:20 2017 -0400 +++ b/kaks_analysis.xml Thu Dec 21 09:17:01 2017 -0500 @@ -63,23 +63,42 @@ --max_ks $set_upper_ks_limit_cond.max_ks #end if #end if -&>proc.log -&& mv $output_dir/species1.fna '$output_species1_fna' -&& mv $output_dir/species1.faa '$output_species1_faa' -#if str($comparison) == 'paralogs': - && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' - && mv $output_dir/*.rbhb '$output_rbhb_paralog' -#else: - && mv $output_dir/species2.faa '$output_species2_faa' - && mv $output_dir/species2.fna '$output_species2_fna' - && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' - && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' - && mv $output_dir/*.rbhb '$output_rbhb_ortholog' -#end if -&& mv $output_dir/*.kaks '$output_kaks' -#if str($fit_components) == 'yes': - && mv $output_dir/*.components '$output_components' -#end if +&>kaks_analysis_log.txt; +if [[ $? -ne 0 ]]; then + cp kaks_analysis_log.txt '$output_species1_fna'; + cp kaks_analysis_log.txt '$output_species1_faa'; + #if str($comparison) == 'paralogs': + cp kaks_analysis_log.txt '$output_species1_paralog'; + cp kaks_analysis_log.txt '$output_rbhb_paralog'; + #else: + cp kaks_analysis_log.txt '$output_species2_faa'; + cp kaks_analysis_log.txt '$output_species2_fna'; + cp kaks_analysis_log.txt '$output_species1_ortholog'; + cp kaks_analysis_log.txt '$output_species2_ortholog'; + cp kaks_analysis_log.txt '$output_rbhb_ortholog'; + #end if + cp kaks_analysis_log.txt '$output_kaks'; + #if str($fit_components) == 'yes': + cp kaks_analysis_log.txt '$output_components' + #end if +else + && mv $output_dir/species1.fna '$output_species1_fna' + && mv $output_dir/species1.faa '$output_species1_faa' + #if str($comparison) == 'paralogs': + && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog' + && mv $output_dir/*.rbhb '$output_rbhb_paralog' + #else: + && mv $output_dir/species2.faa '$output_species2_faa' + && mv $output_dir/species2.fna '$output_species2_fna' + && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog' + && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog' + && mv $output_dir/*.rbhb '$output_rbhb_ortholog' + #end if + && mv $output_dir/*.kaks '$output_kaks' + #if str($fit_components) == 'yes': + && mv $output_dir/*.components '$output_components' + #end if +fi ]]></command> <inputs> <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences for the first species" />