Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison amplicon_analysis_pipeline.xml @ 46:8d5fe964f61f draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 06b2cc0d518a6a4d77b865b6567e0bc6a2fb26df
author pjbriggs
date Wed, 11 Dec 2019 13:59:48 +0000
parents 4bfa62618f7c
children dac038bd896d
comparison
equal deleted inserted replaced
45:4bfa62618f7c 46:8d5fe964f61f
68 && 68 &&
69 69
70 ## Collect outputs 70 ## Collect outputs
71 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" && 71 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
72 #if str( $pipeline_name ) == "Vsearch" 72 #if str( $pipeline_name ) == "Vsearch"
73 # Vsearch-specific 73 ## Vsearch-specific
74 cp ${pipeline_name}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" && 74 cp ${pipeline_name}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
75 cp Multiplexed_files/${pipeline_name}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" && 75 cp Multiplexed_files/${pipeline_name}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
76 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" && 76 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
77 #else 77 #else
78 # DADA2-specific 78 ## DADA2-specific
79 cp ${pipeline_name}_OTU_tables/DADA2_tax_OTU_table.biom "${tax_otu_table_biom_file}" && 79 cp ${pipeline_name}_OTU_tables/DADA2_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
80 cp ${pipeline_name}_OTU_tables/seqs.fa "${dereplicated_nonchimera_otus_fasta}" && 80 cp ${pipeline_name}_OTU_tables/seqs.fa "${dereplicated_nonchimera_otus_fasta}" &&
81 #end if 81 #end if
82 cp ${pipeline_name}_OTU_tables/otus.tre "${otus_tre_file}" && 82 cp ${pipeline_name}_OTU_tables/otus.tre "${otus_tre_file}" &&
83 cp RESULTS/${pipeline_name}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" && 83 cp RESULTS/${pipeline_name}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&