# HG changeset patch # User iuc # Date 1495181639 14400 # Node ID 10ea852bc26dbd9e1dda1cee71a81638659a6aae # Parent 20194da2549deb0993b2d52082e010ba042424a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit e5d24fc90f811c8994ec8b72371ab4100d2c294c diff -r 20194da2549d -r 10ea852bc26d generate_test_data.sh.orig --- a/generate_test_data.sh.orig Fri May 19 03:54:05 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,312 +0,0 @@ -#!/usr/bin/env bash - -# 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 - -# 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 - -# 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 - -# 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 - -# core_diversity_analyses -# Data are from test data in https://github.com/biocore/qiime -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 - -# 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 - -# 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 - -#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 - -##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 - -# 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 - -#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 - -# 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 -<<<<<<< HEAD -======= - -# 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' ->>>>>>> Update of the Qiime_core generate_test_data script