comparison generate_test_data.sh @ 3:bb0c29df7392 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380

2:45b4946c4458

    --suppress_taxa_summary \
    --suppress_beta_diversity \
    --suppress_alpha_diversity \
    --suppress_group_significance
rm -rf core_diversity_analyses_2

# filter_alignment
filter_alignment.py \
    --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
    -o 'filter_alignment_default' \

cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'
rm -rf split_libraries

# 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

# 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'

3:bb0c29df7392

    --suppress_taxa_summary \
    --suppress_beta_diversity \
    --suppress_alpha_diversity \
    --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' \
    -o 'filter_alignment_default' \

cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'
rm -rf split_libraries

# split_libraries_fastq
split_libraries_fastq.py \
    --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
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'
cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt'