Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

diff outputs.txt @ 4:86a12d75ebe4 draft default tip

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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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/outputs.txt	Fri Dec 20 06:59:49 2019 -0500
@@ -0,0 +1,41 @@
+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?)