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view generate_test_data.sh @ 1:c5a99b5e2c19 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 03:54:47 -0400 |
parents | f9df45b8425a |
children | b63216cf3245 |
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#!/usr/bin/env bash # Data are from test data in https://github.com/biocore/qiime # align_seqs align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_pynast_uclust' \ --alignment_method 'pynast' \ --pairwise_alignment_method 'uclust' \ --template_fp 'test-data/align_seqs/core_set_aligned.fasta.imputed' \ --min_percent_id '0.75' align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_pynast_muscle' \ --alignment_method 'pynast' \ --pairwise_alignment_method 'muscle' \ --min_length '50' \ --min_percent_id '0.75' align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_pynast_pair_hmm' \ --alignment_method 'pynast' \ --pairwise_alignment_method 'pair_hmm' \ --min_percent_id '0.75' #align_seqs.py \ # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ # -o 'align_seqs_pynast_clustal' \ # --alignment_method 'pynast' \ # --pairwise_alignment_method 'clustal' \ # --min_percent_id '0.75' align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_pynast_blast' \ --alignment_method 'pynast' \ --pairwise_alignment_method 'blast' \ --min_percent_id '0.75' align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_pynast_mafft' \ --alignment_method 'pynast' \ --pairwise_alignment_method 'mafft' \ --min_percent_id '0.75' #align_seqs.py \ # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ # -o 'align_seqs_infernal' \ # --alignment_method 'infernal' \ # --template_fp 'test-data/align_seqs/seed.16s.reference_model.sto' \ # --min_percent_id '0.75' #align_seqs.py \ # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ # -o 'align_seqs_clustalw' \ # --alignment_method 'clustalw' \ # --min_percent_id '0.75' align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_muscle' \ --alignment_method 'muscle' \ --min_percent_id '0.75' align_seqs.py \ --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ -o 'align_seqs_mafft' \ --alignment_method 'mafft' \ --min_percent_id '0.75' #alpha_rarefaction alpha_rarefaction.py \ --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \ --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \ -o alpha_rarefaction \ --num_steps '2' \ --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \ --min_rare_depth '10' \ --max_rare_depth '50' \ --retain_intermediate_files rm -rf alpha_rarefaction # assign_taxonomy assign_taxonomy.py \ --input_fasta_fp 'test-data/assign_taxonomy/uclust_input_seqs.fasta' \ --assignment_method 'uclust' \ --min_consensus_fraction '0.51' \ --similarity '0.9' \ --uclust_max_accepts '3' \ -o assign_taxonomy_uclust cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt 'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt' rm -rf assign_taxonomy_uclust #assign_taxonomy.py \ # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \ # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \ # --assignment_method 'rdp' \ # --confidence '3' \ # -o assign_taxonomy_rdp #assign_taxonomy.py \ # --input_fasta_fp 'test-data/assign_taxonomy/rtax_ref_seq_set.fna' \ # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt' \ # --assignment_method 'rtax' \ # --read_1_seqs_fp 'test-data/assign_taxonomy/read_1.seqs.fna' \ # --read_2_seqs_fp 'test-data/assign_taxonomy/read_2.seqs.fna' \ # --single_ok \ # --no_single_ok_generic \ # --read_id_regex "\S+\s+(\S+)" \ # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \ # --header_id_regex "\S+\s+(\S+?)\/" \ # -o assign_taxonomy_rtax #ls assign_taxonomy_rtax #assign_taxonomy.py \ # --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ # --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ # --assignment_method 'mothur' \ # --confidence 0.5 \ # -o assign_taxonomy_mothur #ls assign_taxonomy_mothur assign_taxonomy.py \ --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ --assignment_method 'sortmerna' \ --min_consensus_fraction "0.51" \ --similarity "0.9" \ --sortmerna_e_value "1.0" \ --sortmerna_coverage "0.9" \ --sortmerna_best_N_alignments "5" \ -o assign_taxonomy_sortmerna cp assign_taxonomy_sortmerna/sortmerna_map.blast 'test-data/assign_taxonomy/sortmerna_map.blast' cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt 'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt' rm -rf assign_taxonomy_sortmerna #beta_diversity beta_diversity.py \ --input_path 'test-data/beta_diversity/otu_table.biom' \ -o beta_diversity_1 \ --metrics 'unweighted_unifrac,weighted_unifrac' \ --tree_path 'test-data/beta_diversity/rep_set.tre' md5 'beta_diversity_1/unweighted_unifrac_otu_table.txt' md5 'beta_diversity_1/weighted_unifrac_otu_table.txt' rm -rf beta_diversity_1 beta_diversity.py \ --input_path 'test-data/beta_diversity/otu_table.biom' \ -o beta_diversity_2 \ --metrics 'abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac_g,unifrac_g_full_tree,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac' \ --tree_path 'test-data/beta_diversity/rep_set.tre' md5 'beta_diversity_2/canberra_otu_table.txt' md5 'beta_diversity_2/pearson_otu_table.txt' rm -rf beta_diversity_2 #beta_diversity_through_plots beta_diversity_through_plots.py \ --otu_table_fp 'test-data/beta_diversity_through_plots/otu_table.biom' \ --mapping_fp 'test-data/beta_diversity_through_plots/map.txt' \ --output_dir beta_diversity_through_plots \ --tree_fp 'test-data/beta_diversity_through_plots/rep_set.tre' \ --parallel cp beta_diversity_through_plots/unweighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/' cp beta_diversity_through_plots/unweighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/' cp beta_diversity_through_plots/weighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/' cp beta_diversity_through_plots/weighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/' rm -rf beta_diversity_through_plots # compare_categories compare_categories.py \ --method 'adonis' \ --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \ --mapping_file 'test-data/compare_categories/map.txt' \ --categories 'Treatment' \ -o compare_categories_1 \ --num_permutations '999' cp compare_categories_1/adonis_results.txt "test-data/compare_categories/adonis_results.txt" rm -rf compare_categories_1 compare_categories.py \ --method 'dbrda' \ --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \ --mapping_file 'test-data/compare_categories/map.txt' \ --categories 'Treatment' \ -o compare_categories_2 \ --num_permutations '99' cp compare_categories_2/* "test-data/compare_categories/" rm -rf compare_categories_2 # core_diversity_analyses core_diversity_analyses.py \ --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \ -o core_diversity_analyses_1 \ --mapping_fp 'test-data/core_diversity_analyses/map.txt' \ --sampling_depth 22 \ --tree_fp 'test-data/core_diversity_analyses/rep_set.tre' cp core_diversity_analyses_1/bdiv_even22/unweighted_unifrac_pc.txt 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' rm -rf core_diversity_analyses_1 core_diversity_analyses.py \ --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \ -o core_diversity_analyses_2 \ --mapping_fp 'test-data/core_diversity_analyses/map.txt' \ --sampling_depth 22 \ --nonphylogenetic_diversity \ --suppress_taxa_summary \ --suppress_beta_diversity \ --suppress_alpha_diversity \ --suppress_group_significance rm -rf core_diversity_analyses_2 # filter_alignment filter_alignment.py \ --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ -o 'filter_alignment_default' \ --allowed_gap_frac '0.999999' \ --threshold '3.0' filter_alignment.py \ --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ -o 'filter_alignment_without_mask_filter_and_outliers' \ --suppress_lane_mask_filter \ --allowed_gap_frac '0.999999' \ --remove_outliers \ --threshold '3.0' filter_alignment.py \ --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ -o 'filter_alignment_entropy' \ --allowed_gap_frac '0.999999' \ --threshold '3.0' \ --entropy_threshold '0.1' # filter_fasta filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_otu_map.fasta' \ --otu_map 'test-data/filter_fasta/otu_map.txt' filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_otu_map_negate.fasta' \ --otu_map 'test-data/filter_fasta/otu_map.txt' \ --negate filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_seq_id.fasta' \ --seq_id_fp 'test-data/filter_fasta/seqs_to_keep.txt' filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_otu_table.fasta' \ --biom_fp 'test-data/filter_fasta/otu_table.biom' filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_subject_fasta.fasta' \ --subject_fasta_fp 'test-data/filter_fasta/sl_inseqs.fasta' filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_seq_id_prefix.fasta' \ --seq_id_prefix 'S5' filter_fasta.py \ --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ --output_fasta_fp 'filter_fasta_sample_id.fasta' \ --sample_id_fp 'test-data/filter_fasta/map.txt' # filter_otus_from_otu_table filter_otus_from_otu_table.py \ --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ --min_count '2' \ --max_count '1000' \ --min_samples '5' \ --max_samples '350' \ --output_fp 'test-data/filter_otus_from_otu_table/filtered_otu_table.biom' filter_otus_from_otu_table.py \ --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \ --output_fp 'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom' filter_otus_from_otu_table.py \ --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \ --negate_ids_to_exclude \ --output_fp 'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom' # filter_samples_from_otu_table filter_samples_from_otu_table.py \ --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ --min_count '150' biom convert \ -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ -o 'test-data/filter_samples_from_otu_table/abundance_min.biom' \ --to-json rm 'test-data/filter_samples_from_otu_table/tmp.biom' filter_samples_from_otu_table.py \ --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ --min_count '0' \ --max_count '149' biom convert \ -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ -o 'test-data/filter_samples_from_otu_table/abundance_max.biom' \ --to-json rm 'test-data/filter_samples_from_otu_table/tmp.biom' filter_samples_from_otu_table.py \ --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \ --output_mapping_fp 'test-data/filter_samples_from_otu_table/metadata_positive.txt' \ -s 'Treatment:Control' biom convert \ -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ -o 'test-data/filter_samples_from_otu_table/metadata_positive.biom' \ --to-json rm 'test-data/filter_samples_from_otu_table/tmp.biom' filter_samples_from_otu_table.py \ --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \ -s 'Treatment:*,!Control' biom convert \ -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ -o 'test-data/filter_samples_from_otu_table/metadata_negative.biom' \ --to-json rm 'test-data/filter_samples_from_otu_table/tmp.biom' filter_samples_from_otu_table.py \ --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' biom convert \ -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ -o 'test-data/filter_samples_from_otu_table/id_positive.biom' \ --to-json rm 'test-data/filter_samples_from_otu_table/tmp.biom' filter_samples_from_otu_table.py \ --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' \ --negate_sample_id_fp biom convert \ -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ -o 'test-data/filter_samples_from_otu_table/id_negative.biom' \ --to-json rm 'test-data/filter_samples_from_otu_table/tmp.biom' # filter_taxa_from_otu_table filter_taxa_from_otu_table.py \ --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ --positive_taxa 'p__Bacteroidetes,p__Firmicutes' \ --metadata_field 'taxonomy' biom convert \ -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ -o 'test-data/filter_taxa_from_otu_table/positive_taxa.biom' \ --to-json rm 'test-data/filter_taxa_from_otu_table/tmp.biom' filter_taxa_from_otu_table.py \ --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ --negative_taxa 'p__Bacteroidetes,p__Firmicutes' \ --metadata_field 'taxonomy' biom convert \ -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ -o 'test-data/filter_taxa_from_otu_table/negative_taxa.biom' \ --to-json rm 'test-data/filter_taxa_from_otu_table/tmp.biom' filter_taxa_from_otu_table.py \ --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ --positive_taxa 'p__Firmicutes' \ --negative_taxa 'c__Clostridia' \ --metadata_field 'taxonomy' biom convert \ -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ -o 'test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom' \ --to-json rm 'test-data/filter_taxa_from_otu_table/tmp.biom' # jackknifed_beta_diversity jackknifed_beta_diversity.py \ --otu_table_fp 'test-data/jackknifed_beta_diversity/otu_table.biom' \ --mapping_fp 'test-data/jackknifed_beta_diversity/map.txt' \ -o jackknifed_beta_diversity \ --seqs_per_sample '10' \ --tree_fp 'test-data/jackknifed_beta_diversity/rep_set.tre' \ --master_tree 'consensus' \ --parallel rm -rf jackknifed_beta_diversity # make_emperor cp 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' 'test-data/make_emperor/unweighted_unifrac_pc.txt' cp 'test-data/core_diversity_analyses/map.txt' 'test-data/make_emperor/map.txt' cp 'test-data/summarize_taxa/2_L3.txt' 'test-data/make_emperor/2_L3.txt' make_emperor.py \ --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \ -o make_emperor_1 \ --map_fp 'test-data/make_emperor/map.txt' \ --number_of_axes '10' \ --add_unique_columns \ --number_of_segments 8 rm -rf make_emperor_1 make_emperor.py \ --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \ -o make_emperor_2 \ --map_fp 'test-data/make_emperor/map.txt' \ --number_of_axes '10' \ --add_unique_columns \ --number_of_segments 8 \ --taxa_fp 'test-data/make_emperor/2_L3.txt' \ --n_taxa_to_keep 10 rm -rf make_emperor_2 # make_otu_heatmap make_otu_heatmap.py \ --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ --imagetype 'pdf' \ --color_scheme "YlGn" \ --width "5" \ --height "5" \ --dpi "200" \ --obs_md_category "taxonomy" \ --output_fp 'test-data/make_otu_heatmap/basic_heatmap.pdf' make_otu_heatmap.py \ --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ --imagetype 'png' \ --color_scheme "YlGn" \ --width "5" \ --height "5" \ --dpi "200" \ --obs_md_category "taxonomy" \ --output_fp 'test-data/make_otu_heatmap/basic_heatmap.png' make_otu_heatmap.py \ --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ --imagetype 'svg' \ --color_scheme "YlGn" \ --width "5" \ --height "5" \ --dpi "200" \ --obs_md_category "taxonomy" \ --output_fp 'test-data/make_otu_heatmap/basic_heatmap.svg' make_otu_heatmap.py \ --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ --imagetype 'pdf' \ --color_scheme "YlGn" \ --width "5" \ --height "5" \ --dpi "200" \ --obs_md_category "taxonomy" \ --output_fp 'test-data/make_otu_heatmap/sample_sorted_heatmap.pdf' make_otu_heatmap.py \ --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ --otu_tree 'test-data/make_otu_heatmap/rep_set.tre' \ --imagetype 'pdf' \ --color_scheme "YlGn" \ --width "5" \ --height "5" \ --dpi "200" \ --obs_md_category "taxonomy" \ --output_fp 'test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf' make_otu_heatmap.py \ --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ --category "Treatment" \ --imagetype 'pdf' \ --color_scheme "YlGn" \ --width "5" \ --height "5" \ --dpi "200" \ --obs_md_category "taxonomy" \ --output_fp 'test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf' # make_phylogeny make_phylogeny.py \ --input_fp 'test-data/make_phylogeny/aligned.fasta' \ --result_fp 'test-data/make_phylogeny/fasttree_tree_method_default.tre' \ --tree_method 'fasttree' \ --log_fp 'fasttree_tree_method_default.txt' \ --root_method 'tree_method_default' make_phylogeny.py \ --input_fp 'test-data/make_phylogeny/aligned.fasta' \ --result_fp 'raxml_v730.tre' \ --tree_method 'raxml_v730' \ --log_fp 'raxml_v730.txt' \ --root_method 'tree_method_default' make_phylogeny.py \ --input_fp 'test-data/make_phylogeny/aligned.fasta' \ --result_fp 'test-data/make_phylogeny/muscle.tre' \ --tree_method 'muscle' \ --log_fp 'muscle.txt' \ --root_method 'tree_method_default' make_phylogeny.py \ --input_fp 'test-data/make_phylogeny/aligned.fasta' \ --result_fp 'test-data/make_phylogeny/clustalw.tre' \ --tree_method 'clustalw' \ --log_fp 'clustalw.txt' \ --root_method 'tree_method_default' make_phylogeny.py \ --input_fp 'test-data/make_phylogeny/aligned.fasta' \ --result_fp 'clearcut.tre' \ --tree_method 'clearcut' \ --log_fp 'clearcut.txt' \ --root_method 'tree_method_default' make_phylogeny.py \ --input_fp 'test-data/make_phylogeny/aligned.fasta' \ --result_fp 'test-data/make_phylogeny/fasttree_midpoint.tre' \ --tree_method 'fasttree' \ --log_fp 'fasttree_midpoint.txt' \ --root_method 'midpoint' # multiple_join_paired_ends multiple_join_paired_ends.py \ --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \ --output_dir 'test-data/multiple_join_paired_ends/output_without_barcode' \ --read1_indicator 'forward_' \ --read2_indicator 'reverse_' \ --leading_text '' \ --trailing_text '' #multiple_join_paired_ends.py \ # --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \ # --output_dir 'multiple_join_paired_ends_without_barcode_parameter_files' \ # --parameter_fp 'test-data/multiple_join_paired_ends/qiime_parameters.txt' \ # --read1_indicator '_R1_' \ # --read2_indicator '_R2_' \ # --leading_text '' \ # --trailing_text '' multiple_join_paired_ends.py \ --input_dir 'test-data/multiple_join_paired_ends/with_barcode/' \ --output_dir 'test-data/multiple_join_paired_ends/output_with_barcode' \ --read1_indicator 'forward_' \ --read2_indicator 'reverse_' \ --match_barcodes \ --barcode_indicator 'barcode_' \ --leading_text '' \ --trailing_text '' # multiple_split_libraries_fastq multiple_split_libraries_fastq.py \ --input_dir 'test-data/multiple_split_libraries_fastq/input' \ --output_dir 'multiple_split_libraries_fastq' \ --demultiplexing_method 'mapping_barcode_files' \ --read_indicator 'reads_' \ --barcode_indicator 'barcodes_' \ --mapping_indicator 'mapping_' \ --mapping_extensions 'txt' \ --leading_text '' \ --trailing_text '' \ --sampleid_indicator '.' multiple_split_libraries_fastq.py \ --input_dir 'test-data/multiple_split_libraries_fastq/input' \ --output_dir 'multiple_split_libraries_fastq_with_parameter_file' \ --demultiplexing_method 'mapping_barcode_files' \ --parameter_fp 'test-data/multiple_split_libraries_fastq/qiime_parameters.txt' \ --read_indicator 'reads_' \ --barcode_indicator 'barcodes_' \ --mapping_indicator 'mapping_' \ --mapping_extensions 'txt' \ --leading_text '' \ --trailing_text '' \ --sampleid_indicator '.' # pick_closed_reference_otus pick_closed_reference_otus.py \ --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ --output_dir 'pick_closed_reference_otus' \ --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' biom convert \ -i 'pick_closed_reference_otus/otu_table.biom' \ -o 'test-data/pick_closed_reference_otus/basic_otu_table.biom' \ --to-json pick_closed_reference_otus.py \ --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ --output_dir 'pick_closed_reference_otus_sortmerna' \ --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' \ --parameter_fp 'test-data/pick_closed_reference_otus/sortmerna_params.txt' biom convert \ -i 'pick_closed_reference_otus_sortmerna/otu_table.biom' \ -o 'test-data/pick_closed_reference_otus/sortmerna_otu_table.biom' \ --to-json pick_closed_reference_otus.py \ --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ --output_dir 'pick_closed_reference_otus_assign_taxonomy' \ --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ --assign_taxonomy biom convert \ -i 'pick_closed_reference_otus_assign_taxonomy/otu_table.biom' \ -o 'test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom' \ --to-json pick_closed_reference_otus.py \ --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ --output_dir 'pick_closed_reference_otus_suppress_taxonomy_assignment' \ --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ --suppress_taxonomy_assignment biom convert \ -i 'pick_closed_reference_otus_suppress_taxonomy_assignment/otu_table.biom' \ -o 'test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom' \ --to-json # pick_open_reference_otus pick_open_reference_otus.py \ --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ -o pick_open_reference_otus_1 \ --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ --otu_picking_method 'uclust' \ --new_ref_set_id 'New' \ --parallel \ --percent_subsample '0.001' \ --prefilter_percent_id '0.0' \ --minimum_failure_threshold '100000' \ --min_otu_size '2' cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt' cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt' cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre' rm -rf pick_open_reference_otus_1 pick_open_reference_otus.py \ --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ -o pick_open_reference_otus_2 \ --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ --otu_picking_method 'uclust' \ --new_ref_set_id 'New' \ --parallel \ --percent_subsample '0.001' \ --prefilter_percent_id '0.0' \ --minimum_failure_threshold '100000' \ --min_otu_size '3' \ --suppress_taxonomy_assignment \ --suppress_align_and_tree cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt' cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt' rm -rf pick_open_reference_otus_2 pick_open_reference_otus.py \ --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ -o pick_open_reference_otus_3 \ --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ --otu_picking_method 'uclust' \ --new_ref_set_id 'New' \ --parallel \ --percent_subsample '0.001' \ --prefilter_percent_id '0.0' \ --minimum_failure_threshold '100000' \ --min_otu_size '10' \ --suppress_taxonomy_assignment cp pick_open_reference_otus_3/final_otu_map.txt 'test-data/pick_open_reference_otus/3_final_otu_map.txt' cp pick_open_reference_otus_3/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/3_final_otu_map_mc.txt' cp pick_open_reference_otus_3/rep_set.tre 'test-data/pick_open_reference_otus/3_rep_set_tree.tre' rm -rf pick_open_reference_otus_3 # pick_otus pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_uclust' \ --otu_picking_method 'uclust' \ --similarity "0.97" \ --denovo_otu_id_prefix "denovo" \ --max_accepts "1" \ --max_rejects "8" \ --stepwords "8" \ --word_length "8" \ --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_sortmerna' \ --otu_picking_method "sortmerna" \ --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ --sortmerna_e_value "1" \ --sortmerna_coverage "0.97" \ --sortmerna_tabular \ --sortmerna_best_N_alignments "1" \ --sortmerna_max_pos "10000" \ --similarity "0.97" \ --non_chimeras_retention "union" #pick_otus.py \ # -i 'test-data/pick_otus/seqs.fna' \ # -o 'pick_otus_mothur' \ # --otu_picking_method "mothur" \ # --clustering_algorithm "furthest" \ # --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_trie' \ --otu_picking_method "trie" \ --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_uclust_ref' \ --otu_picking_method "uclust_ref" \ --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ --similarity "0.97" \ --max_accepts "1" \ --max_rejects "8" \ --stepwords "8" \ --word_length "8" \ --non_chimeras_retention "union" #pick_otus.py \ # -i 'test-data/pick_otus/seqs.fna' \ # -o 'pick_otus_blast' \ # --otu_picking_method "blast" \ # --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ # --similarity "0.97" \ # --max_e_value_blast "1e-10" \ # --min_aligned_percent "0.5" \ # --non_chimeras_retention "union" # pick_otus.py \ # -i 'test-data/pick_otus/seqs.fna' \ # -o 'pick_otus_sumaclust' \ # --otu_picking_method "sumaclust" \ # --similarity "0.97" \ # --sumaclust_l \ # --denovo_otu_id_prefix "denovo" \ # --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_swarm' \ --otu_picking_method "swarm" \ --denovo_otu_id_prefix "denovo" \ --swarm_resolution "1" \ --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_prefix_suffix' \ --otu_picking_method "prefix_suffix" \ --prefix_length "50" \ --suffix_length "50" \ --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_cdhit' \ --otu_picking_method "cdhit" \ --similarity "0.97" \ --non_chimeras_retention "union" pick_otus.py \ -i 'test-data/pick_otus/seqs.fna' \ -o 'pick_otus_uclust_intersection' \ --otu_picking_method "uclust" \ --similarity "0.97" \ --denovo_otu_id_prefix "denovo" \ --max_accepts "1" \ --max_rejects "8" \ --stepwords "8" \ --word_length "8" \ --non_chimeras_retention "intersection" # pick_rep_set pick_rep_set.py \ --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ --fasta_file 'test-data/pick_rep_set/seqs.fna' \ --rep_set_picking_method 'first' \ --sort_by 'otu' \ --result_fp 'test-data/pick_rep_set/first_otu_fasta.fasta' \ --log_fp 'test-data/pick_rep_set/first_otu_fasta.txt' pick_rep_set.py \ --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ --fasta_file 'test-data/pick_rep_set/seqs.fna' \ --reference_seqs_fp 'test-data/pick_rep_set/refseqs.fasta' \ --rep_set_picking_method 'first' \ --sort_by 'otu' \ --result_fp 'test-data/pick_rep_set/first_otu_fasta_ref.fasta' \ --log_fp 'test-data/pick_rep_set/first_otu_fasta_ref.txt' pick_rep_set.py \ --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ --fasta_file 'test-data/pick_rep_set/seqs.fna' \ --rep_set_picking_method 'longest' \ --sort_by 'otu' \ --result_fp 'test-data/pick_rep_set/longest_otu_fasta.fasta' \ --log_fp 'test-data/pick_rep_set/longest_otu_fasta.txt' pick_rep_set.py \ --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ --fasta_file 'test-data/pick_rep_set/seqs.fna' \ --rep_set_picking_method 'most_abundant' \ --sort_by 'otu' \ --result_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.fasta' \ --log_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.txt' pick_rep_set.py \ --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ --fasta_file 'test-data/pick_rep_set/seqs.fna' \ --rep_set_picking_method 'random' \ --sort_by 'otu' \ --result_fp 'test-data/pick_rep_set/random_otu_fasta.fasta' \ --log_fp 'test-data/pick_rep_set/random_otu_fasta.txt' pick_rep_set.py \ --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ --fasta_file 'test-data/pick_rep_set/seqs.fna' \ --rep_set_picking_method 'first' \ --sort_by 'seq_id' \ --result_fp 'test-data/pick_rep_set/first_seq_id_fasta.fasta' \ --log_fp 'test-data/pick_rep_set/first_seq_id_fasta.txt' # plot_taxa_summary plot_taxa_summary.py \ --counts_fname 'test-data/plot_taxa_summary/phylum.txt' \ --dir_path 'test-data/plot_taxa_summary/phylum' \ --labels 'phylum' \ --num_categories '20' \ --background_color 'white' \ --dpi '80' \ --x_width '12' \ --y_height '12' \ --bar_width '0.75' \ --type_of_file 'png' \ --chart_type 'area,bar,pie' \ --resize_nth_label '0' \ --label_type 'categorical' plot_taxa_summary.py \ --counts_fname 'test-data/plot_taxa_summary/phylum.txt,test-data/plot_taxa_summary/class.txt,test-data/plot_taxa_summary/genus.txt' \ --dir_path 'test-data/plot_taxa_summary/phylum_class_genus' \ --labels 'Phylum,Class,Genus' \ --num_categories '20' \ --background_color 'white' \ --dpi '80' \ --x_width '12' \ --y_height '12' \ --bar_width '0.75' \ --type_of_file 'png' \ --chart_type 'area,bar,pie' \ --resize_nth_label '0' \ --label_type 'categorical' plot_taxa_summary.py \ --counts_fname 'test-data/plot_taxa_summary/class.txt' \ --dir_path 'test-data/plot_taxa_summary/class' \ --labels 'Class' \ --num_categories '10' \ --background_color 'white' \ --dpi '80' \ --x_width '12' \ --y_height '12' \ --bar_width '0.75' \ --chart_type 'pie' \ --type_of_file 'svg' \ --include_html_legend \ --resize_nth_label '0' \ --label_type 'categorical' plot_taxa_summary.py \ --counts_fname 'test-data/plot_taxa_summary/class.txt' \ --dir_path 'test-data/plot_taxa_summary/class_colorby' \ --labels 'Class' \ --num_categories '20' \ --colorby 'PC.636,PC.635' \ --background_color 'white' \ --dpi '80' \ --x_width '12' \ --y_height '12' \ --bar_width '0.75' \ --type_of_file 'pdf' \ --chart_type 'area,bar,pie' \ --resize_nth_label '0' \ --label_type 'categorical' # split_libraries split_libraries.py \ --map 'test-data/split_libraries/mapping_file.txt' \ -o split_libraries \ --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \ --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \ --min_qual_score 25 \ --qual_score_window 0 \ --record_qual_scores \ --min_seq_length 200 \ --max_seq_length 1000 \ --max_ambig 6 \ --max_homopolymer 6 \ --max_primer_mismatch 0 \ --barcode_type 'golay_12' \ --max_barcode_errors 1.5 \ --start_numbering_at 1 cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna' cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log' cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt' cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual' rm -rf split_libraries # split_libraries_fastq split_libraries_fastq.py \ --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \ -o split_libraries \ --mapping_fps 'test-data/map.tsv' \ --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \ --store_qual_scores \ --store_demultiplexed_fastq \ --max_bad_run_length 3 \ --min_per_read_length_fraction 0.75 \ --sequence_max_n 0 \ --start_seq_id 0 \ --barcode_type 'golay_12' \ --max_barcode_errors 1.5 cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular' cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta' cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual' cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq' rm -rf split_libraries # summarize_taxa cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom' cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt' summarize_taxa.py \ -i 'test-data/summarize_taxa/otu_table.biom' \ -o summarize_taxa_1 \ -L '2,3,4,5,6' \ -m 'test-data/summarize_taxa/map.txt' \ --md_identifier "taxonomy" \ --delimiter ";" cp summarize_taxa_1/*_L2.txt "test-data/summarize_taxa/1_L2.txt" cp summarize_taxa_1/*_L3.txt "test-data/summarize_taxa/1_L3.txt" cp summarize_taxa_1/*_L4.txt "test-data/summarize_taxa/1_L4.txt" cp summarize_taxa_1/*_L5.txt "test-data/summarize_taxa/1_L5.txt" cp summarize_taxa_1/*_L6.txt "test-data/summarize_taxa/1_L6.txt" rm -rf summarize_taxa_1 summarize_taxa.py \ -i 'test-data/summarize_taxa/otu_table.biom' \ -o summarize_taxa_2 \ -L '3,6' \ --md_identifier "taxonomy" \ --delimiter ";" cp summarize_taxa_2/*_L3.txt "test-data/summarize_taxa/2_L3.txt" cp summarize_taxa_2/*_L6.txt "test-data/summarize_taxa/2_L6.txt" rm -rf summarize_taxa_2 # summarize_taxa_through_plots summarize_taxa_through_plots.py \ --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ --output_dir summarize_taxa_through_plots_mapping \ --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' biom convert \ -i 'summarize_taxa_through_plots_mapping/otu_table_L2.biom' \ -o 'summarize_taxa_through_plots_mapping/otu_table_L2_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping/otu_table_L3.biom' \ -o 'summarize_taxa_through_plots_mapping/otu_table_L3_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping/otu_table_L4.biom' \ -o 'summarize_taxa_through_plots_mapping/otu_table_L4_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping/otu_table_L5.biom' \ -o 'summarize_taxa_through_plots_mapping/otu_table_L5_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping/otu_table_L6.biom' \ -o 'summarize_taxa_through_plots_mapping/otu_table_L6_json.biom' \ --to-json cp summarize_taxa_through_plots_mapping/*.txt test-data/summarize_taxa_through_plots/mapping/ cp summarize_taxa_through_plots_mapping/*_json.biom test-data/summarize_taxa_through_plots/mapping/ cp summarize_taxa_through_plots_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping/area_charts.html' cp summarize_taxa_through_plots_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping/bar_charts.html' summarize_taxa_through_plots.py \ --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ --output_dir summarize_taxa_through_plots_mapping_categories \ --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \ --mapping_category 'Treatment' biom convert \ -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.biom' \ -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.biom' \ -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.biom' \ -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.biom' \ -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.biom' \ -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6_json.biom' \ --to-json cp summarize_taxa_through_plots_mapping_categories/*.txt test-data/summarize_taxa_through_plots/mapping_categories/ cp summarize_taxa_through_plots_mapping_categories/*_json.biom test-data/summarize_taxa_through_plots/mapping_categories/ cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html' cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html' summarize_taxa_through_plots.py \ --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ --output_dir summarize_taxa_through_plots_mapping_sort \ --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \ --sort biom convert \ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \ -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \ --to-json cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/ cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/ cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html' cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html' summarize_taxa_through_plots.py \ --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ --output_dir summarize_taxa_through_plots_without_mapping biom convert \ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \ --to-json biom convert \ -i 'summarize_taxa_through_plots_without_mapping/otu_table_L6.biom' \ -o 'summarize_taxa_through_plots_without_mapping/otu_table_L6_json.biom' \ --to-json cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/ cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/ cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html' cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html' # upgma_cluster upgma_cluster.py \ --input_path 'test-data/upgma_cluster/' \ --output_path 'test-data/upgma_cluster/' # validate_mapping_file validate_mapping_file.py \ -m 'test-data/validate_mapping_file/map.tsv' \ -o validate_mapping_file_output \ -c '_' cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html' cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log' cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt' rm -rf validate_mapping_file_output