| Previous changeset 1:56bb6d26af5a (2017-05-19) Next changeset 3:8e0af6dd18ba (2017-06-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit e5d24fc90f811c8994ec8b72371ab4100d2c294c |
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removed:
generate_test_data.sh.orig |
| b |
| diff -r 56bb6d26af5a -r 74880d08445c generate_test_data.sh.orig --- a/generate_test_data.sh.orig Fri May 19 03:49:37 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b"@@ -1,312 +0,0 @@\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' |