Mercurial > repos > iuc > qiime_align_seqs

comparison generate_test_data.sh @ 5:98614f0549e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:17:14 -0400
parents 7d11451e92b8
children
comparison
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4:141dcdf14479 5:98614f0549e3
225 --suppress_taxa_summary \ 225 --suppress_taxa_summary \
226 --suppress_beta_diversity \ 226 --suppress_beta_diversity \
227 --suppress_alpha_diversity \ 227 --suppress_alpha_diversity \
228 --suppress_group_significance 228 --suppress_group_significance
229 rm -rf core_diversity_analyses_2 229 rm -rf core_diversity_analyses_2
230
231 # extract_barcodes
232 extract_barcodes.py \
233 --fastq1 'test-data/extract_barcodes/inseqs.fastq' \
234 --input_type 'barcode_single_end' \
235 -o extract_barcodes_1 \
236 --bc1_len '6' \
237 --rev_comp_bc1
238 rm -rf extract_barcodes_1
239
240 extract_barcodes.py \
241 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
242 --input_type 'barcode_paired_end' \
243 --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \
244 -o extract_barcodes_2 \
245 --bc1_len '6' \
246 --bc2_len '6'
247 rm -rf extract_barcodes_2
248
249 extract_barcodes.py \
250 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
251 --input_type 'barcode_paired_end' \
252 --fastq2 'test-data/extract_barcodes/inseqs_R2.fastq' \
253 -o extract_barcodes_3 \
254 --bc1_len '6' \
255 --bc2_len '6' \
256 --mapping_fp 'test-data/extract_barcodes/mapping_data.txt' \
257 --attempt_read_reorientation \
258 --disable_header_match
259 rm -rf extract_barcodes_3
260
261 extract_barcodes.py \
262 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
263 --input_type 'barcode_paired_stitched' \
264 -o extract_barcodes_4 \
265 --bc1_len '6' \
266 --bc2_len '8' \
267 --rev_comp_bc1 \
268 --rev_comp_bc2
269 rm -rf extract_barcodes_4
270
271 extract_barcodes.py \
272 --fastq1 'test-data/extract_barcodes/inseqs_R1.fastq' \
273 --input_type 'barcode_in_label' \
274 --char_delineator '#' \
275 -o extract_barcodes_5 \
276 --bc1_len '6'
277 rm -rf extract_barcodes_5
230 278
231 # filter_alignment 279 # filter_alignment
232 filter_alignment.py \ 280 filter_alignment.py \
233 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ 281 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
234 -o 'filter_alignment_default' \ 282 -o 'filter_alignment_default' \
941 cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual' 989 cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'
942 rm -rf split_libraries 990 rm -rf split_libraries
943 991
944 # split_libraries_fastq 992 # split_libraries_fastq
945 split_libraries_fastq.py \ 993 split_libraries_fastq.py \
946 --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \ 994 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
947 -o split_libraries \ 995 -o split_libraries_1 \
948 --mapping_fps 'test-data/map.tsv' \ 996 --mapping_fps 'test-data/split_libraries_fastq/map.txt' \
949 --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \ 997 --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \
998 --max_bad_run_length 3 \
999 --min_per_read_length_fraction 0.75 \
1000 --sequence_max_n 0 \
1001 --start_seq_id 0 \
1002 --rev_comp_mapping_barcodes \
1003 --phred_quality_threshold 19 \
1004 --barcode_type 'golay_12' \
1005 --max_barcode_errors 1.5
1006 rm -rf split_libraries_1
1007
1008 split_libraries_fastq.py \
1009 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
1010 -o split_libraries_2 \
1011 --mapping_fps 'test-data/split_libraries_fastq/map.txt' \
1012 --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz' \
950 --store_qual_scores \ 1013 --store_qual_scores \
951 --store_demultiplexed_fastq \ 1014 --store_demultiplexed_fastq \
952 --max_bad_run_length 3 \ 1015 --max_bad_run_length 3 \
953 --min_per_read_length_fraction 0.75 \ 1016 --min_per_read_length_fraction 0.75 \
954 --sequence_max_n 0 \ 1017 --sequence_max_n 0 \
955 --start_seq_id 0 \ 1018 --start_seq_id 0 \
1019 --rev_comp_mapping_barcodes \
1020 --phred_quality_threshold 19 \
956 --barcode_type 'golay_12' \ 1021 --barcode_type 'golay_12' \
957 --max_barcode_errors 1.5 1022 --max_barcode_errors 1.5
958 cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular' 1023 rm -rf split_libraries_2
959 cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta' 1024
960 cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual' 1025 split_libraries_fastq.py \
961 cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq' 1026 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \
962 rm -rf split_libraries 1027 -o split_libraries_3 \
1028 --mapping_fps 'test-data/split_libraries_fastq/map.txt,test-data/split_libraries_fastq/map.txt' \
1029 --barcode_read_fps 'test-data/split_libraries_fastq/lane1_barcode.fastq.gz,test-data/split_libraries_fastq/lane2_barcode.fastq.gz' \
1030 --max_bad_run_length 3 \
1031 --min_per_read_length_fraction 0.75 \
1032 --sequence_max_n 0 \
1033 --start_seq_id 0 \
1034 --rev_comp_mapping_barcodes \
1035 --phred_quality_threshold 19 \
1036 --barcode_type 'golay_12' \
1037 --max_barcode_errors 1.5
1038 rm -rf split_libraries_3
1039
1040 split_libraries_fastq.py \
1041 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz' \
1042 -o split_libraries_4 \
1043 --sample_ids 'my.sample.1' \
1044 --max_bad_run_length 3 \
1045 --min_per_read_length_fraction 0.75 \
1046 --sequence_max_n 0 \
1047 --start_seq_id 0 \
1048 --rev_comp_mapping_barcodes \
1049 --phred_quality_threshold 19 \
1050 --barcode_type 'not-barcoded' \
1051 --max_barcode_errors 1.5
1052 rm -rf split_libraries_4
1053
1054 split_libraries_fastq.py \
1055 --sequence_read_fps 'test-data/split_libraries_fastq/lane1_read1.fastq.gz,test-data/split_libraries_fastq/lane2_read1.fastq.gz' \
1056 -o split_libraries_5 \
1057 --sample_ids 'my.sample.1,my.sample.2' \
1058 --max_bad_run_length 3 \
1059 --min_per_read_length_fraction 0.75 \
1060 --sequence_max_n 0 \
1061 --start_seq_id 0 \
1062 --rev_comp_mapping_barcodes \
1063 --phred_quality_threshold 19 \
1064 --barcode_type 'not-barcoded' \
1065 --max_barcode_errors 1.5
1066 rm -rf split_libraries_5
963 1067
964 # summarize_taxa 1068 # summarize_taxa
965 cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom' 1069 cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom'
966 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt' 1070 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt'
967 1071