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annotate biom_convert.xml @ 3:bd46669113b9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 3a3e9549dbaa39d32a8fe1f709a9aa89f2f55e72"
author iuc
date Sat, 26 Jun 2021 19:09:19 +0000
parents 584008e574b2
children 54ccb7e1f49a
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3
bd46669113b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 3a3e9549dbaa39d32a8fe1f709a9aa89f2f55e72"
iuc
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1 <tool id="biom_convert" name="Convert" version="@VERSION@.4">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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2 <description>between BIOM table formats</description>
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3 <macros>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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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
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5 </macros>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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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
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7 <expand macro="version_command" />
1
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8 <command detect_errors="exit_code">
0
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9 <![CDATA[
1
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10 ## biom convert requires the header to start with a #
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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11 ## so we just add one if its missing
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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12 #if $input.type_selector == "tsv"
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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13 sed '1s/^\([^#].*\)/#\1/' '$input.input_fp' > input &&
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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14 #else
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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15 ln -s '$input.input_fp' input &&
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501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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16 #end if
1
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17 biom convert
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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18 --input-fp input
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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19 --output-fp '$output_fp'
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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20 #if str( $input.type_selector ) == "tsv"
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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21 #if $input.process_obs_metadata:
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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22 --process-obs-metadata '$input.process_obs_metadata'
0
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23 #end if
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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24 #end if
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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25 #if str( $output.type_selector ) == "tsv"
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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26 --to-tsv
2
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27 #if $output.header_key
1
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28 --header-key '$output.header_key'
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29 #if $output.output_metadata_id
1
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30 --output-metadata-id '$output.output_metadata_id'
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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31 #end if
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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32 --tsv-metadata-formatter '$output.tsv_metadata_formatter'
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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33 #end if
0
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34 #else:
1
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35 --table-type '$output.table_type'
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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36 #if str( $output.biom_type.selector ) == 'hdf5':
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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37 --to-hdf5
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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38 $output.biom_type.collapsed_samples
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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39 $output.biom_type.collapsed_observations
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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40 #else:
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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41 --to-json
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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42 #end if
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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43 #if $output.sample_metadata_fp
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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44 --sample-metadata-fp '$output.sample_metadata_fp'
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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45 #end if
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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46 #if $output.observation_metadata_fp
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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47 --observation-metadata-fp '$output.observation_metadata_fp'
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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48 #end if
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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49 #end if
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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50 ]]>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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51 </command>
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52 <inputs>
1
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53 <conditional name="input">
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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54 <param name="type_selector" type="select" label="Choose the source BIOM format">
0
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55 <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
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56 <option value="biom">BIOM File</option>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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57 </param>
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58 <when value="tsv">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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59 <param name="input_fp" argument="--input-fp" type="data" format="tabular" label="Input table" />
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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60 <param name="process_obs_metadata" argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting">
0
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61 <option value="" selected="True">Do Not process metadata</option>
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62 <option value="taxonomy">taxonomy</option>
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63 <option value="naive">naive</option>
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64 <option value="sc_separated">sc_separated</option>
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65 </param>
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66 </when>
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67 <when value="biom">
1
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68 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/>
0
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69 </when>
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70 </conditional>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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71 <conditional name="output">
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72 <param name="type_selector" type="select" label="Choose the output type">
0
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73 <option value="tsv">TSV-formatted (classic) table</option>
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74 <option value="biom" selected="True">BIOM</option>
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75 </param>
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76 <when value="tsv">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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77 <param name="header_key" argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" />
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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78 <param name="output_metadata_id" argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" />
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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79 <param name="tsv_metadata_formatter" argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" >
0
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80 <option value="naive" selected="True">naive</option>
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81 <option value="sc_separated">Semi-colon separated</option>
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82 </param>
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83 </when>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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84 <when value="biom">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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85 <param name="table_type" argument="--table-type" type="select" label="Table Type" >
0
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86 <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
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87 <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
88 <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
89 <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
90 <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
91 <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
92 <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
93 <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
94 </param>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
95 <conditional name="biom_type">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
96 <param name="selector" type="select" label="BIOM format type">
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
97 <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
98 <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
99 </param>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
100 <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
101 </when>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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102 <when value="hdf5">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
103 <param name="collapsed_observations" argument="--collapsed-observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples"/>
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
104 <param name="collapsed_samples" argument="--collapsed-samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
105 </when>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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106 </conditional>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
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107 <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" />
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
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108 <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" />
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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109 </when>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
110 </conditional>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
111 </inputs>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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112 <outputs>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
113 <data format="biom1" name="output_fp">
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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114 <change_format>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
115 <when input="output.type_selector" value="tsv" format="tabular" />
3
bd46669113b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 3a3e9549dbaa39d32a8fe1f709a9aa89f2f55e72"
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parents: 2
diff changeset
116 <when input="output.biom_type" value="json" format="biom1" />
bd46669113b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 3a3e9549dbaa39d32a8fe1f709a9aa89f2f55e72"
iuc
parents: 2
diff changeset
117 <when input="output.biom_type" value="hdf5" format="biom2" />
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
118 </change_format>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
119 </data>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
120 </outputs>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
121 <tests>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
122 <test>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
123 <conditional name="input">
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
124 <param name="type_selector" value="tsv"/>
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
125 <param name="input_fp" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/>
0
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="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:
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127 </conditional>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
128 <conditional name="output">
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
129 <param name="type_selector" value="biom"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
130 <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
131 <conditional name="biom_type">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
132 <param name="selector" value="json"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
133 </conditional>
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="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
135 <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
136 </conditional>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
137 <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
138 </test>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
139 <test>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
140 <conditional name="input">
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
141 <param name="type_selector" value="tsv"/>
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
142 <param name="input_fp" value="input_abundance_1.tabular" ftype="tabular"/>
0
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="process_obs_metadata" value=""/>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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144 </conditional>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
145 <conditional name="output">
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
146 <param name="type_selector" value="biom"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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147 <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:
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148 <conditional name="biom_type">
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
149 <param name="selector" value="json"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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150 </conditional>
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
151 <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
152 <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:
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153 </conditional>
1
0de92f0b96ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
154 <output name="output_fp" file="output_1.biom1.re" ftype="biom1" compare="re_match"/>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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155 </test>
2
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
156 <test>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
157 <conditional name="input">
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
158 <param name="type_selector" value="biom"/>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
159 <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
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160 </conditional>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
161 <conditional name="output">
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
162 <param name="type_selector" value="tsv"/>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
163 <param name="header_key"/>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
164 <param name="output_metadata_id"/>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
165 <param name="tsv_metadata_formatter" value="naive"/>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
166 </conditional>
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
167 <output name="output_fp" file="output_abundance_1.tabular" ftype="tabular" />
584008e574b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f1b3e36f79747fca391321389276ac196d3f7cd0"
iuc
parents: 1
diff changeset
168 </test>
0
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
169 </tests>
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iuc
parents:
diff changeset
170 <help><![CDATA[
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parents:
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171
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iuc
parents:
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172 Usage: biom convert [OPTIONS]::
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173
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
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174 Convert to/from the BIOM table format.
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175
501c21cce614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
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176 Convert between BIOM table formats. See examples here: http://biom-format.org/documentation/biom_conversion.html
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177
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178 Example usage:
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180 Convert a "classic" BIOM file (tab-separated text) to an HDF5 BIOM formatted OTU table:
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181
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182 $ biom convert -i table.txt -o table.biom --to-hdf5
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183
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184
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185 Options:
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186 -i, --input-fp PATH The input BIOM table [required]
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187 -o, --output-fp PATH The output BIOM table [required]
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188 -m, --sample-metadata-fp PATH The sample metadata mapping file (will add sample metadata to the input BIOM table, if provided).
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189 --observation-metadata-fp PATH The observation metadata mapping file (will add observation metadata to the input BIOM table, if provided).
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190 --to-json Output as JSON-formatted table.
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191 --to-hdf5 Output as HDF5-formatted table.
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192 --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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193 --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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194 --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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195 --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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196 --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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197 --process-obs-metadata taxonomy,naive,sc_separated Process metadata associated with observations when converting from a classic table.
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198 --tsv-metadata-formatter naive,sc_separated Method for formatting the observation
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199 --help Show this message and exit.
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200
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201 ]]></help>
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202 <expand macro="citations" />
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203 </tool>