| Previous changeset 0:51ce498c97f4 (2017-05-18) Next changeset 2:a0d2430136e6 (2017-05-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d |
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added:
generate_test_data.sh.orig |
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| diff -r 51ce498c97f4 -r 3616af4c6531 generate_test_data.sh.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh.orig Fri May 19 03:59:42 2017 -0400 |
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| b"@@ -0,0 +1,312 @@\n+#!/usr/bin/env bash\n+\n+# validate_mapping_file\n+validate_mapping_file.py \\\n+ -m 'test-data/validate_mapping_file/map.tsv' \\\n+ -o validate_mapping_file_output \\\n+ -c '_'\n+cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html'\n+cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log'\n+cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt'\n+rm -rf validate_mapping_file_output\n+\n+# split_libraries_fastq\n+split_libraries_fastq.py \\\n+ --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \\\n+ -o split_libraries \\\n+ --mapping_fps 'test-data/map.tsv' \\\n+ --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \\\n+ --store_qual_scores \\\n+ --store_demultiplexed_fastq \\\n+ --max_bad_run_length 3 \\\n+ --min_per_read_length_fraction 0.75 \\\n+ --sequence_max_n 0 \\\n+ --start_seq_id 0 \\\n+ --barcode_type 'golay_12' \\\n+ --max_barcode_errors 1.5\n+cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular'\n+cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta'\n+cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual'\n+cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq'\n+rm -rf split_libraries\n+\n+# split_libraries\n+split_libraries.py \\\n+ --map 'test-data/split_libraries/mapping_file.txt' \\\n+ -o split_libraries \\\n+ --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \\\n+ --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \\\n+ --min_qual_score 25 \\\n+ --qual_score_window 0 \\\n+ --record_qual_scores \\\n+ --min_seq_length 200 \\\n+ --max_seq_length 1000 \\\n+ --max_ambig 6 \\\n+ --max_homopolymer 6 \\\n+ --max_primer_mismatch 0 \\\n+ --barcode_type 'golay_12' \\\n+ --max_barcode_errors 1.5 \\\n+ --start_numbering_at 1\n+cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna'\n+cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log'\n+cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt'\n+cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'\n+rm -rf split_libraries\n+\n+# pick_open_reference_otus\n+pick_open_reference_otus.py \\\n+ --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \\\n+ -o pick_open_reference_otus_1 \\\n+ --reference_fp 'test-data/gg_13_8_79_otus.fasta' \\\n+ --otu_picking_method 'uclust' \\\n+ --new_ref_set_id 'New' \\\n+ --parallel \\\n+ --percent_subsample '0.001' \\\n+ --prefilter_percent_id '0.0' \\\n+ --minimum_failure_threshold '100000' \\\n+ --min_otu_size '2'\n+cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt'\n+cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt'\n+cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre'\n+rm -rf pick_open_reference_otus_1\n+\n+pick_open_reference_otus.py \\\n+ --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \\\n+ -o pick_open_reference_otus_2 \\\n+ --reference_fp 'test-data/gg_13_8_79_otus.fasta' \\\n+ --otu_picking_method 'uclust' \\\n+ --new_ref_set_id 'New' \\\n+ --parallel \\\n+ --percent_subsample '0.001' \\\n+ --prefilter_percent_id '0.0' \\\n+ --minimum_failure_threshold '100000' \\\n+ --min_otu_size '3' \\\n+ --suppress_taxonomy_assignment \\\n+ --suppress_align_and_tree\n+cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt'\n+cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt'\n+rm -rf pick_open_reference_otus_2\n+\n+pick_open_reference_otus.py \\\n+ --input_fps 'test-data/pick_open"..b'rsity\n+\n+#beta_diversity_through_plots\n+beta_diversity_through_plots.py \\\n+ --otu_table_fp \'test-data/beta_diversity_through_plots/otu_table.biom\' \\\n+ --mapping_fp \'test-data/beta_diversity_through_plots/map.txt\' \\\n+ --output_dir beta_diversity_through_plots \\\n+ --tree_fp \'test-data/beta_diversity_through_plots/rep_set.tre\' \\\n+ --parallel\n+cp beta_diversity_through_plots/unweighted_unifrac_dm.txt \'test-data/beta_diversity_through_plots/\'\n+cp beta_diversity_through_plots/unweighted_unifrac_pc.txt \'test-data/beta_diversity_through_plots/\'\n+cp beta_diversity_through_plots/weighted_unifrac_dm.txt \'test-data/beta_diversity_through_plots/\'\n+cp beta_diversity_through_plots/weighted_unifrac_pc.txt \'test-data/beta_diversity_through_plots/\'\n+rm -rf beta_diversity_through_plots\n+\n+# assign_taxonomy\n+assign_taxonomy.py \\\n+ --input_fasta_fp \'test-data/assign_taxonomy/uclust_input_seqs.fasta\' \\\n+ --assignment_method \'uclust\' \\\n+ --min_consensus_fraction \'0.51\' \\\n+ --similarity \'0.9\' \\\n+ --uclust_max_accepts \'3\' \\\n+ -o assign_taxonomy_uclust\n+cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt \'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt\'\n+rm -rf assign_taxonomy_uclust\n+\n+#assign_taxonomy.py \\\n+# --input_fasta_fp \'test-data/assign_taxonomy/rdp_input_seqs.fasta\' \\\n+# --id_to_taxonomy_fp \'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt\' \\\n+# --assignment_method \'rdp\' \\\n+# --confidence \'3\' \\\n+# -o assign_taxonomy_rdp\n+\n+#assign_taxonomy.py \\\n+# --input_fasta_fp \'test-data/assign_taxonomy/rtax_ref_seq_set.fna\' \\\n+# --id_to_taxonomy_fp \'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt\' \\\n+# --assignment_method \'rtax\' \\\n+# --read_1_seqs_fp \'test-data/assign_taxonomy/read_1.seqs.fna\' \\\n+# --read_2_seqs_fp \'test-data/assign_taxonomy/read_2.seqs.fna\' \\\n+# --single_ok \\\n+# --no_single_ok_generic \\\n+# --read_id_regex "\\S+\\s+(\\S+)" \\\n+# --amplicon_id_regex "(\\S+)\\s+(\\S+?)\\/" \\\n+# --header_id_regex "\\S+\\s+(\\S+?)\\/" \\\n+# -o assign_taxonomy_rtax\n+#ls assign_taxonomy_rtax\n+\n+#assign_taxonomy.py \\\n+# --input_fasta_fp \'test-data/assign_taxonomy/mothur_ref_seq_set.fna\' \\\n+# --id_to_taxonomy_fp \'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt\' \\\n+# --assignment_method \'mothur\' \\\n+# --confidence 0.5 \\\n+# -o assign_taxonomy_mothur\n+#ls assign_taxonomy_mothur\n+\n+assign_taxonomy.py \\\n+ --input_fasta_fp \'test-data/assign_taxonomy/mothur_ref_seq_set.fna\' \\\n+ --assignment_method \'sortmerna\' \\\n+ --min_consensus_fraction "0.51" \\\n+ --similarity "0.9" \\\n+ --sortmerna_e_value "1.0" \\\n+ --sortmerna_coverage "0.9" \\\n+ --sortmerna_best_N_alignments "5" \\\n+ -o assign_taxonomy_sortmerna\n+cp assign_taxonomy_sortmerna/sortmerna_map.blast \'test-data/assign_taxonomy/sortmerna_map.blast\'\n+cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt \'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt\'\n+rm -rf assign_taxonomy_sortmerna\n+<<<<<<< HEAD\n+=======\n+\n+# filter_otus_from_otu_table\n+filter_otus_from_otu_table.py \\\n+ --input_fp \'test-data/filter_otus_from_otu_table/otu_table.biom\' \\\n+ --min_count \'2\' \\\n+ --max_count \'1000\' \\\n+ --min_samples \'5\' \\\n+ --max_samples \'350\' \\\n+ --output_fp \'test-data/filter_otus_from_otu_table/filtered_otu_table.biom\'\n+\n+filter_otus_from_otu_table.py \\\n+ --input_fp \'test-data/filter_otus_from_otu_table/otu_table.biom\' \\\n+ --otu_ids_to_exclude_fp \'test-data/filter_otus_from_otu_table/chimeric_otus.txt\' \\\n+ --output_fp \'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom\'\n+\n+filter_otus_from_otu_table.py \\\n+ --input_fp \'test-data/filter_otus_from_otu_table/otu_table.biom\' \\\n+ --otu_ids_to_exclude_fp \'test-data/filter_otus_from_otu_table/chimeric_otus.txt\' \\\n+ --negate_ids_to_exclude \\\n+ --output_fp \'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom\'\n+>>>>>>> Update of the Qiime_core generate_test_data script\n' |