Mercurial > repos > iuc > qiime_collapse_samples
view 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 |
| parents | |
| children |
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#!/usr/bin/env bash # make_otu_table make_otu_table.py \ --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \ --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \ --exclude_otus_fp 'test-data/make_otu_table/chimeric_seqs.txt' \ --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \ --output_biom_fp 'test-data/make_otu_table/OTU_table_chimeric.biom' biom convert \ -i 'test-data/make_otu_table/OTU_table_chimeric.biom' \ -o 'test-data/make_otu_table/OTU_table_chimeric.biom' \ --to-json make_otu_table.py \ --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \ --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \ --exclude_otus_fp 'test-data/make_otu_table/pynast_failures.fna' \ --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \ --output_biom_fp 'test-data/make_otu_table/OTU_table_pynast.biom' biom convert \ -i 'test-data/make_otu_table/OTU_table_pynast.biom' \ -o 'test-data/make_otu_table/OTU_table_pynast.biom' \ --to-json # collapse_samples collapse_samples.py \ --input_biom_fp 'test-data/collapse_samples/table.biom' \ --mapping_fp 'test-data/collapse_samples/map.txt' \ --collapse_mode 'sum' \ --collapse_fields 'SampleType' \ --output_biom_fp 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \ --output_mapping_fp 'test-data/collapse_samples/collapsed_sum_SampleType_map.txt' biom convert \ -i 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \ -o 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \ --to-json collapse_samples.py \ --input_biom_fp 'test-data/collapse_samples/table.biom' \ --mapping_fp 'test-data/collapse_samples/map.txt' \ --collapse_mode 'first' \ --collapse_fields 'subject','year' \ --normalize \ --output_biom_fp 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \ --output_mapping_fp 'test-data/collapse_samples/collapsed_first_2fields_map.txt' biom convert \ -i 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \ -o 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \ --to-json