Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate outputs.txt @ 44:213b5cdecb70 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit a0f1569b4882ca4f9cee613615fe75771bbf0b23-dirty
author pjbriggs
date Mon, 09 Dec 2019 13:00:31 +0000
parents 098ad1dd7760
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
42
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
1 ok.. Metatable_log/Metatable_mod.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
2 ok.. Vsearch_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
3 ok.. Vsearch_OTU_tables/otus.tre
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
4 ok.. RESULTS/Vsearch_gg/OTUs_count.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
5 ok.. RESULTS/Vsearch_gg/table_summary.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
6 ok.. Multiplexed_files/Vsearch_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
7 ok.. QUALITY_CONTROL/Reads_count.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
8 ok.. fastqc_quality_boxplots.html -> generated by the Python wrapper
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
9 NO.. RESULTS/Vsearch_gg/Heatmap/js -> RESULTS/Vsearch_gg/Heatmap.pdf
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
10 NO.. RESULTS/Vsearch_gg/Heatmap/otu_table.html -> MISSING
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
11 ok.. RESULTS/Vsearch_gg/phylum_genus_charts/charts/
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
12 ok.. RESULTS/Vsearch_gg/phylum_genus_charts/raw_data/
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
13 ok.. RESULTS/Vsearch_gg/phylum_genus_charts/bar_charts.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
14 ok.. RESULTS/Vsearch_gg/beta_div_even/weighted_2d_plot/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
15 ok.. RESULTS/Vsearch_gg/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
16 ok.. RESULTS/Vsearch_gg/beta_div_even/unweighted_2d_plot/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
17 ok.. RESULTS/Vsearch_gg/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
18 ok.. RESULTS/Vsearch_gg/Alpha_diversity/rarefaction_curves/rarefaction_plots.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
19 ok.. RESULTS/Vsearch_gg/Alpha_diversity/rarefaction_curves/average_plots
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
20 ok.. RESULTS/Vsearch_gg/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
21
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
22 ??.. Metatable_log/Metatable_mod.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
23 NO.. DADA2_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
24 ok.. DADA2_OTU_tables/otus.tre
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
25 ok.. RESULTS/DADA2_silva/OTUs_count.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
26 ok.. RESULTS/DADA2_silva/table_summary.txt
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
27 ok.. Multiplexed_files/DADA2_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta --> DADA2_OTU_tables/seqs.fa
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
28 NO.. QUALITY_CONTROL/Reads_count.txt -> Vsearch only
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
29 ok.. fastqc_quality_boxplots.html -> generated by the Python wrapper
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
30 NO.. RESULTS/DADA2_silva/Heatmap/js -> RESULTS/DADA2_silva/Heatmap.pdf
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
31 NO.. RESULTS/DADA2_silva/Heatmap/otu_table.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
32 ok.. RESULTS/DADA2_silva/phylum_genus_charts/charts/
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
33 ok.. RESULTS/DADA2_silva/phylum_genus_charts/raw_data/
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
34 ok.. RESULTS/DADA2_silva/phylum_genus_charts/bar_charts.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
35 ok.. RESULTS/DADA2_silva/beta_div_even/weighted_2d_plot/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
36 ok.. RESULTS/DADA2_silva/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
37 ok.. RESULTS/DADA2_silva/beta_div_even/unweighted_2d_plot/*
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
38 ok.. RESULTS/DADA2_silva/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
39 ok.. RESULTS/DADA2_silva/Alpha_diversity/rarefaction_curves/rarefaction_plots.html
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
40 ok.. RESULTS/DADA2_silva/Alpha_diversity/rarefaction_curves/average_plots
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
pjbriggs
parents:
diff changeset
41 ok.. RESULTS/DADA2_silva/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf -> missing? (didn't include categories?)