Mercurial > repos > iuc > qiime_align_seqs

changeset 1:fd82f36a0c59 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 03:39:36 -0400
parents 56adf8db7ce7
children adb832fbff2c
files generate_test_data.sh.orig
diffstat 1 files changed, 312 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_test_data.sh.orig	Fri May 19 03:39:36 2017 -0400
@@ -0,0 +1,312 @@
+#!/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