Mercurial > repos > iuc > qiime_collapse_samples

annotate generate_test_data.sh @ 0:14f1d71dcab3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
author iuc
date Mon, 10 Jul 2017 16:25:42 -0400
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14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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1 #!/usr/bin/env bash
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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2
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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3 # make_otu_table
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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4 make_otu_table.py \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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5 --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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6 --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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7 --exclude_otus_fp 'test-data/make_otu_table/chimeric_seqs.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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8 --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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9 --output_biom_fp 'test-data/make_otu_table/OTU_table_chimeric.biom'
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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10 biom convert \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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11 -i 'test-data/make_otu_table/OTU_table_chimeric.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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12 -o 'test-data/make_otu_table/OTU_table_chimeric.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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13 --to-json
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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14
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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15 make_otu_table.py \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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16 --otu_map_fp 'test-data/make_otu_table/otu_map.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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17 --taxonomy 'test-data/make_otu_table/tax_assignments.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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18 --exclude_otus_fp 'test-data/make_otu_table/pynast_failures.fna' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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19 --mapping_fp 'test-data/make_otu_table/mapping_file.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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20 --output_biom_fp 'test-data/make_otu_table/OTU_table_pynast.biom'
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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21 biom convert \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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22 -i 'test-data/make_otu_table/OTU_table_pynast.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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23 -o 'test-data/make_otu_table/OTU_table_pynast.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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24 --to-json
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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26 # collapse_samples
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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27 collapse_samples.py \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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28 --input_biom_fp 'test-data/collapse_samples/table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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29 --mapping_fp 'test-data/collapse_samples/map.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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30 --collapse_mode 'sum' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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31 --collapse_fields 'SampleType' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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32 --output_biom_fp 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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33 --output_mapping_fp 'test-data/collapse_samples/collapsed_sum_SampleType_map.txt'
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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34 biom convert \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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35 -i 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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36 -o 'test-data/collapse_samples/collapsed_sum_SampleType_table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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37 --to-json
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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38
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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39 collapse_samples.py \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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40 --input_biom_fp 'test-data/collapse_samples/table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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41 --mapping_fp 'test-data/collapse_samples/map.txt' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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42 --collapse_mode 'first' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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43 --collapse_fields 'subject','year' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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44 --normalize \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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45 --output_biom_fp 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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46 --output_mapping_fp 'test-data/collapse_samples/collapsed_first_2fields_map.txt'
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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47 biom convert \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
iuc
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48 -i 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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49 -o 'test-data/collapse_samples/collapsed_first_2fields_table.biom' \
14f1d71dcab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
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50 --to-json