Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8
author pjbriggs
date Fri, 20 Dec 2019 06:59:49 -0500
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ok.. Metatable_log/Metatable_mod.txt
ok.. Vsearch_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom
ok.. Vsearch_OTU_tables/otus.tre
ok.. RESULTS/Vsearch_gg/OTUs_count.txt
ok.. RESULTS/Vsearch_gg/table_summary.txt
ok.. Multiplexed_files/Vsearch_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta
ok.. QUALITY_CONTROL/Reads_count.txt
ok.. fastqc_quality_boxplots.html -> generated by the Python wrapper
NO.. RESULTS/Vsearch_gg/Heatmap/js -> RESULTS/Vsearch_gg/Heatmap.pdf
NO.. RESULTS/Vsearch_gg/Heatmap/otu_table.html -> MISSING
ok.. RESULTS/Vsearch_gg/phylum_genus_charts/charts/
ok.. RESULTS/Vsearch_gg/phylum_genus_charts/raw_data/
ok.. RESULTS/Vsearch_gg/phylum_genus_charts/bar_charts.html
ok.. RESULTS/Vsearch_gg/beta_div_even/weighted_2d_plot/*
ok.. RESULTS/Vsearch_gg/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html
ok.. RESULTS/Vsearch_gg/beta_div_even/unweighted_2d_plot/*
ok.. RESULTS/Vsearch_gg/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html
ok.. RESULTS/Vsearch_gg/Alpha_diversity/rarefaction_curves/rarefaction_plots.html
ok.. RESULTS/Vsearch_gg/Alpha_diversity/rarefaction_curves/average_plots
ok.. RESULTS/Vsearch_gg/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf

??.. Metatable_log/Metatable_mod.txt
NO.. DADA2_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom
ok.. DADA2_OTU_tables/otus.tre
ok.. RESULTS/DADA2_silva/OTUs_count.txt
ok.. RESULTS/DADA2_silva/table_summary.txt
ok.. Multiplexed_files/DADA2_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta --> DADA2_OTU_tables/seqs.fa
NO.. QUALITY_CONTROL/Reads_count.txt -> Vsearch only
ok.. fastqc_quality_boxplots.html -> generated by the Python wrapper
NO.. RESULTS/DADA2_silva/Heatmap/js -> RESULTS/DADA2_silva/Heatmap.pdf
NO.. RESULTS/DADA2_silva/Heatmap/otu_table.html
ok.. RESULTS/DADA2_silva/phylum_genus_charts/charts/
ok.. RESULTS/DADA2_silva/phylum_genus_charts/raw_data/
ok.. RESULTS/DADA2_silva/phylum_genus_charts/bar_charts.html
ok.. RESULTS/DADA2_silva/beta_div_even/weighted_2d_plot/*
ok.. RESULTS/DADA2_silva/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html
ok.. RESULTS/DADA2_silva/beta_div_even/unweighted_2d_plot/*
ok.. RESULTS/DADA2_silva/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html
ok.. RESULTS/DADA2_silva/Alpha_diversity/rarefaction_curves/rarefaction_plots.html
ok.. RESULTS/DADA2_silva/Alpha_diversity/rarefaction_curves/average_plots
ok.. RESULTS/DADA2_silva/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf -> missing? (didn't include categories?)