Mercurial > repos > iuc > qiime_make_otu_table
diff generate_test_data.sh @ 0:e00b6983b175 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 16:39:15 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Mon Jul 10 16:39:15 2017 -0400 @@ -0,0 +1,50 @@ +#!/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 \ No newline at end of file