Mercurial > repos > iuc > qiime_count_seqs
diff generate_test_data.sh @ 3:bb0c29df7392 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
---|---|
date | Sat, 05 Aug 2017 07:29:25 -0400 |
parents | abd8e8ffe64d |
children |
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--- a/generate_test_data.sh Mon Jul 10 16:44:52 2017 -0400 +++ b/generate_test_data.sh Sat Aug 05 07:29:25 2017 -0400 @@ -228,6 +228,54 @@ --suppress_group_significance rm -rf core_diversity_analyses_2 +# extract_barcodes +extract_barcodes.py \ + --fastq1 'test-data/extract_barcodes/inseqs.fastq' \ + --input_type 'barcode_single_end' \ + -o extract_barcodes_1 \ + --bc1_len '6' \ + --rev_comp_bc1 +rm -rf extract_barcodes_1 + +extract_barcodes.py \ + --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \ + --input_type 'barcode_paired_end' \ + --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \ + -o extract_barcodes_2 \ + --bc1_len '6' \ + --bc2_len '6' +rm -rf extract_barcodes_2 + +extract_barcodes.py \ + --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \ + --input_type 'barcode_paired_end' \ + --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \ + -o extract_barcodes_3 \ + --bc1_len '6' \ + --bc2_len '6' \ + --mapping_fp 'test-data/extract_barcodes/mapping_data.txt' \ + --attempt_read_reorientation \ + --disable_header_match +rm -rf extract_barcodes_3 + +extract_barcodes.py \ + --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \ + --input_type 'barcode_paired_stitched' \ + -o extract_barcodes_4 \ + --bc1_len '6' \ + --bc2_len '8' \ + --rev_comp_bc1 \ + --rev_comp_bc2 +rm -rf extract_barcodes_4 + +extract_barcodes.py \ + --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \ + --input_type 'barcode_in_label' \ + --char_delineator '#' \ + -o extract_barcodes_5 \ + --bc1_len '6' +rm -rf extract_barcodes_5 + # filter_alignment filter_alignment.py \ --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ @@ -943,23 +991,79 @@ # 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' \ + --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \ + -o split_libraries_1 \ + --mapping_fps 'test-data/split_libraries_fastq/map.txt' \ + --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \ + --max_bad_run_length 3 \ + --min_per_read_length_fraction 0.75 \ + --sequence_max_n 0 \ + --start_seq_id 0 \ + --rev_comp_mapping_barcodes \ + --phred_quality_threshold 19 \ + --barcode_type 'golay_12' \ + --max_barcode_errors 1.5 +rm -rf split_libraries_1 + +split_libraries_fastq.py \ + --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \ + -o split_libraries_2 \ + --mapping_fps 'test-data/split_libraries_fastq/map.txt' \ + --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \ --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 \ + --rev_comp_mapping_barcodes \ + --phred_quality_threshold 19 \ + --barcode_type 'golay_12' \ + --max_barcode_errors 1.5 +rm -rf split_libraries_2 + +split_libraries_fastq.py \ + --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \ + -o split_libraries_3 \ + --mapping_fps 'test-data/split_libraries_fastq/map.txt,test-data/split_libraries_fastq/map.txt' \ + --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz,test-data/split_libraries_fastq/lane2_barcode.fastq.gz' \ + --max_bad_run_length 3 \ + --min_per_read_length_fraction 0.75 \ + --sequence_max_n 0 \ + --start_seq_id 0 \ + --rev_comp_mapping_barcodes \ + --phred_quality_threshold 19 \ --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 +rm -rf split_libraries_3 + +split_libraries_fastq.py \ + --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \ + -o split_libraries_4 \ + --sample_ids 'my.sample.1' \ + --max_bad_run_length 3 \ + --min_per_read_length_fraction 0.75 \ + --sequence_max_n 0 \ + --start_seq_id 0 \ + --rev_comp_mapping_barcodes \ + --phred_quality_threshold 19 \ + --barcode_type 'not-barcoded' \ + --max_barcode_errors 1.5 +rm -rf split_libraries_4 + +split_libraries_fastq.py \ + --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \ + -o split_libraries_5 \ + --sample_ids 'my.sample.1,my.sample.2' \ + --max_bad_run_length 3 \ + --min_per_read_length_fraction 0.75 \ + --sequence_max_n 0 \ + --start_seq_id 0 \ + --rev_comp_mapping_barcodes \ + --phred_quality_threshold 19 \ + --barcode_type 'not-barcoded' \ + --max_barcode_errors 1.5 +rm -rf split_libraries_5 # summarize_taxa cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom'