Mercurial > repos > iuc > biom_convert
annotate biom_convert.xml @ 0:501c21cce614 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
author | iuc |
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date | Tue, 07 Jun 2016 17:26:00 -0400 |
parents | |
children | 0de92f0b96ef |
rev | line source |
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0
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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1 <tool id="biom_convert" name="Convert BIOM" version="@VERSION@.0"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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2 <description>formats</description> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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3 <macros> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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5 </macros> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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6 <expand macro="requirements" /> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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7 <expand macro="stdio" /> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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8 <expand macro="version_command" /> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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9 <command> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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10 <![CDATA[ |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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11 biom convert -i "${input_type.input_table}" -o "${output_table}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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12 #if str( $input_type.input_type_selector ) == "tsv": |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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13 #if $input_type.process_obs_metadata: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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14 --process-obs-metadata "${input_type.process_obs_metadata}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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15 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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16 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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17 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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18 #if str( $output_type.output_type_selector ) == "tsv": |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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19 --to-tsv |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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20 #if $output_type.header_key: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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21 --header-key "${output_type.header_key}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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22 #if $output_type.output_metadata_id: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
23 --output-metadata-id "${output_type.output_metadata_id}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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24 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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25 --tsv-metadata-formatter "${output_type.tsv_metadata_formatter}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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26 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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27 #else: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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28 --table-type "${output_type.table_type}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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29 #if str( $output_type.biom_type.biom_type_selector ) == 'hdf5': |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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30 --to-hdf5 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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31 ${output_type.biom_type.collapsed_samples} |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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32 ${output_type.biom_type.collapsed_observations} |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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33 #else: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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34 --to-json |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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35 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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36 #if $output_type.sample_metadata_fp: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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37 --sample-metadata-fp "${output_type.sample_metadata_fp}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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38 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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39 #if $output_type.observation_metadata_fp: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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40 --observation-metadata-fp "${output_type.observation_metadata_fp}" |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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41 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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42 #end if |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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43 ]]> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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44 </command> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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45 <inputs> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
46 <conditional name="input_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
47 <param name="input_type_selector" type="select" label="Choose the source BIOM format"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
48 <option value="tsv" selected="True">Tabular File</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
49 <option value="biom">BIOM File</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
50 </param> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
51 <when value="tsv"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
52 <param name="input_table" type="data" format="tabular" label="Tabular File" argument="--input-fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
53 <param name="process_obs_metadata" type="select" label="Process metadata associated with observations when converting" argument="--process-obs-metadata"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
54 <option value="" selected="True">Do Not process metadata</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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55 <option value="taxonomy">taxonomy</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
56 <option value="naive">naive</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
57 <option value="sc_separated">sc_separated</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
58 </param> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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59 </when> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
60 <when value="biom"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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61 <param name="input_table" type="data" format="biom1" label="Tabular File" argument="--input-fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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62 </when> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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63 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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64 <conditional name="output_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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65 <param name="output_type_selector" type="select" label="Choose the output type" argument="--to-tsv"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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66 <option value="tsv">TSV-formatted (classic) table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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67 <option value="biom" selected="True">BIOM</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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68 </param> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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69 <when value="tsv"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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70 <param name="header_key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" argument="--header-key"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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71 <param name="output_metadata_id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" argument="--output-metadata-id"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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72 <param name="tsv_metadata_formatter" type="select" label="Method for formatting the observation metadata" argumet="--tsv-metadata-formatter"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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73 <option value="naive" selected="True">naive</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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74 <option value="sc_separated">Semi-colon separated</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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75 </param> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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76 </when> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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77 <when value="biom"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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78 <param name="table_type" type="select" label="Table Type" argument="--table-type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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79 <option value="OTU table">OTU table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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80 <option value="Pathway table">Pathway table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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81 <option value="Function table">Function table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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82 <option value="Ortholog table">Ortholog table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
83 <option value="Gene table">Gene table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
84 <option value="Metabolite table">Metabolite table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
85 <option value="Taxon table">Taxon table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
86 <option value="Table" selected="True">Table</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
87 </param> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
88 <conditional name="biom_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
89 <param name="biom_type_selector" type="select" label="BIOM format type" argument="--to-json / --to-hdf5"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
90 <option value="json" selected="True">JSON-formatted table (BIOM1)</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
91 <option value="hdf5">HDF5-formatted table (BIOM2)</option> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
92 </param> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
93 <when value="json"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
94 </when> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
95 <when value="hdf5"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
96 <param name="collapsed_samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples" argument="--collapsed-observations"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
97 <param name="collapsed_observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
98 </when> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
99 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
100 <param name="sample_metadata_fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" argument="--sample-metadata-fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
101 <param name="observation_metadata_fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" argument="--observation-metadata-fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
102 </when> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
103 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
104 </inputs> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
105 <outputs> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
106 <data format="biom1" name="output_table"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
107 <change_format> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
108 <when input="output_type.output_type_selector" value="tsv" format="tabular" /> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
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109 <when input="output_type.biom_type" value="hdf5" format="biom2" /> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
110 </change_format> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
111 </data> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
112 </outputs> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
113 <tests> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
114 <test> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
115 <conditional name="input_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
116 <param name="input_type_selector" value="tsv"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
117 <param name="input_table" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
118 <param name="process_obs_metadata" value="taxonomy"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
119 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
120 <conditional name="output_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
121 <param name="output_type_selector" value="biom"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
122 <param name="table_type" value="OTU table"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
123 <conditional name="biom_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
124 <param name="biom_type_selector" value="json"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
125 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
126 <param name="sample_metadata_fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
127 <param name="observation_metadata_fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
128 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
129 <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
130 </test> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
131 <test> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
132 <conditional name="input_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
133 <param name="input_type_selector" value="tsv"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
134 <param name="input_table" value="input_abundance_1.tabular" ftype="tabular"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
135 <param name="process_obs_metadata" value=""/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
136 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
137 <conditional name="output_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
138 <param name="output_type_selector" value="biom"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
139 <param name="table_type" value="OTU table"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
140 <conditional name="biom_type"> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
141 <param name="biom_type_selector" value="json"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
142 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
143 <param name="sample_metadata_fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
144 <param name="observation_metadata_fp"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
145 </conditional> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
146 <output name="output_table" file="output_1.biom1.re" ftype="biom1" compare="re_match"/> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
147 </test> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
148 </tests> |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
149 <help><![CDATA[ |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
150 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
151 Usage: biom convert [OPTIONS]:: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
152 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
153 Convert to/from the BIOM table format. |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
154 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
155 Convert between BIOM table formats. See examples here: http://biom-format.org/documentation/biom_conversion.html |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
156 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
157 Example usage: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
158 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
159 Convert a "classic" BIOM file (tab-separated text) to an HDF5 BIOM formatted OTU table: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
160 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
161 $ biom convert -i table.txt -o table.biom --to-hdf5 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
162 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
163 |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
164 Options: |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
165 -i, --input-fp PATH The input BIOM table [required] |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
166 -o, --output-fp PATH The output BIOM table [required] |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
167 -m, --sample-metadata-fp PATH The sample metadata mapping file (will add sample metadata to the input BIOM table, if provided). |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
168 --observation-metadata-fp PATH The observation metadata mapping file (will add observation metadata to the input BIOM table, if provided). |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
169 --to-json Output as JSON-formatted table. |
501c21cce614
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff
changeset
|
170 --to-hdf5 Output as HDF5-formatted table. |
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171 --to-tsv Output as TSV-formatted (classic) table. table is a BIOM table with collapsed samples, this will update the sample metadata of the table to the supported HDF5 collapsed format. |
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172 --collapsed-observations If --to_hdf5 is passed and the original table is a BIOM table with collapsed observations, this will update the supported HDF5 collapsed format. |
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173 --header-key TEXT The observation metadata to include from the input BIOM table file when creating a tsv table file. By default no observation metadata will be included. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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174 --output-metadata-id TEXT The name to be given to the observation metadata column when creating a tsv table file if the column should be renamed. |
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175 --table-type OTU table,Pathway table,Function table,Ortholog table,Gene table,Metabolite table,Taxon table,Table The type of the table. |
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176 --process-obs-metadata taxonomy,naive,sc_separated Process metadata associated with observations when converting from a classic table. |
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177 --tsv-metadata-formatter naive,sc_separated Method for formatting the observation |
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178 --help Show this message and exit. |
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179 |
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180 ]]></help> |
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181 <expand macro="citations" /> |
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182 </tool> |