comparison generate_test_data.sh @ 0:242462fc608b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
author iuc
date Mon, 10 Jul 2017 16:38:55 -0400
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-1:000000000000 0:242462fc608b
1 #!/usr/bin/env bash
2
3 # make_otu_table
4 make_otu_table.py \
5 --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \
6 --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \
7 --exclude_otus_fp 'test-data/make_otu_table/chimeric_seqs.txt' \
8 --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \
9 --output_biom_fp 'test-data/make_otu_table/OTU_table_chimeric.biom'
10 biom convert \
11 -i 'test-data/make_otu_table/OTU_table_chimeric.biom' \
12 -o 'test-data/make_otu_table/OTU_table_chimeric.biom' \
13 --to-json
14
15 make_otu_table.py \
16 --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \
17 --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \
18 --exclude_otus_fp 'test-data/make_otu_table/pynast_failures.fna' \
19 --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \
20 --output_biom_fp 'test-data/make_otu_table/OTU_table_pynast.biom'
21 biom convert \
22 -i 'test-data/make_otu_table/OTU_table_pynast.biom' \
23 -o 'test-data/make_otu_table/OTU_table_pynast.biom' \
24 --to-json
25
26 # collapse_samples
27 collapse_samples.py \
28 --input_biom_fp 'test-data/collapse_samples/table.biom' \
29 --mapping_fp 'test-data/collapse_samples/map.txt' \
30 --collapse_mode 'sum' \
31 --collapse_fields 'SampleType' \
32 --output_biom_fp 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \
33 --output_mapping_fp 'test-data/collapse_samples/collapsed_sum_SampleType_map.txt'
34 biom convert \
35 -i 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \
36 -o 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \
37 --to-json
38
39 collapse_samples.py \
40 --input_biom_fp 'test-data/collapse_samples/table.biom' \
41 --mapping_fp 'test-data/collapse_samples/map.txt' \
42 --collapse_mode 'first' \
43 --collapse_fields 'subject','year' \
44 --normalize \
45 --output_biom_fp 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \
46 --output_mapping_fp 'test-data/collapse_samples/collapsed_first_2fields_map.txt'
47 biom convert \
48 -i 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \
49 -o 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \
50 --to-json