Mercurial > repos > iuc > biom_add_metadata

annotate biom_add_metadata.xml @ 10:3b6f97e7094c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 2230d399cc6a526674f192099f00632dcc931e8c
author iuc
date Fri, 09 Feb 2024 21:36:02 +0000
parents 6ef0b5664c69
children
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1 <tool id="biom_add_metadata" name="Add metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>to a BIOM table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 biom add-metadata
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12 --input-fp '$input_fp'
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13 --output-fp '$output_fp'
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14 #if $sample_metadata_fp
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15 --sample-metadata-fp '$sample_metadata_fp'
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16 #end if
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17 #if $observation_metadata_fp
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18 --observation-metadata-fp '$observation_metadata_fp'
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19 #end if
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20 #if $sc_separated
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21 --sc-separated '$sc_separated'
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22 #end if
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23 #if $sc_pipe_separated
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24 --sc-pipe-separated '$sc_pipe_separated'
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25 #end if
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26 #if $int_fields
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27 --int-fields '$int_fields'
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28 #end if
1
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29 #if $float_fields
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30 --float-fields '$float_fields'
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31 #end if
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32 #if $sample_header
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33 --sample-header '$sample_header'
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34 #end if
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35 #if $observation_header
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36 --observation-header '$observation_header'
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37 #end if
1
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38 $output_as_json
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39 ]]>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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40 </command>
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41 <inputs>
8
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42 <param argument="--input-fp" type="data" format="biom1" label="BIOM File"/>
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43 <param argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" />
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44 <param argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File"/>
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45 <param argument="--sc-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" />
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46 <param argument="--sc-pipe-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)"/>
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47 <param argument="--int-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" />
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48 <param argument="--float-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" />
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49 <param argument="--sample-header" type="text" value="" label="Comma-separated list of the sample metadata field names" />
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50 <param argument="--observation-header" type="text" value="" label="Comma-separated list of the observation metadata field names" />
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51 <param argument="--output-as-json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" />
0
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52 </inputs>
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53 <outputs>
1
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54 <data format="biom1" name="output_fp">
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55 <change_format>
1
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56 <when input="${str( $output_as_json )}" value="" format="h5" />
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57 </change_format>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test>
1
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62 <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/>
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63 <param name="observation_metadata_fp" value="input_taxonomy_1.tabular" ftype="tabular"/>
0
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64 <param name="sc_separated" value="taxonomy"/>
1
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65 <param name="output_as_json" value="--output-as-json"/>
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66 <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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71 Usage: biom add-metadata [OPTIONS]
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72
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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73 Add metadata to a BIOM table.
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74
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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75 Add sample and/or observation metadata to BIOM-formatted files. See
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76 examples here: http://biom-format.org/documentation/adding_metadata.html
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77
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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78 Example usage:
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79
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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80 Add sample metadata to a BIOM table:
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81
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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82 $ biom add-metadata -i otu_table.biom -o table_with_sample_metadata.biom
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83 -m sample_metadata.txt
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84
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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85 Options:
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86 -i, --input-fp PATH The input BIOM table [required]
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87 -o, --output-fp PATH The output BIOM table [required]
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88 -m, --sample-metadata-fp PATH The sample metadata mapping file (will add
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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89 sample metadata to the input BIOM table, if
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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90 provided).
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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91 --observation-metadata-fp PATH The observation metadata mapping file (will
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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92 add observation metadata to the input BIOM
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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93 table, if provided).
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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94 --sc-separated TEXT Comma-separated list of the metadata fields
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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95 to split on semicolons. This is useful for
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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96 hierarchical data such as taxonomy or
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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97 functional categories.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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98 --sc-pipe-separated TEXT Comma-separated list of the metadata fields
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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99 to split on semicolons and pipes ("|"). This
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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100 is useful for hierarchical data such as
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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101 functional categories with one-to-many
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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102 mappings (e.g. x;y;z|x;y;w)).
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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103 --int-fields TEXT Comma-separated list of the metadata fields
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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104 to cast to integers. This is useful for
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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105 integer data such as "DaysSinceStart".
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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106 --float-fields TEXT Comma-separated list of the metadata fields
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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107 to cast to floating point numbers. This is
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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108 useful for real number data such as "pH".
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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109 --sample-header TEXT Comma-separated list of the sample metadata
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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110 field names. This is useful if a header line
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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111 is not provided with the metadata, if you
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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112 want to rename the fields, or if you want to
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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113 include only the first n fields where n is
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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114 the number of entries provided here.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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115 --observation-header TEXT Comma-separated list of the observation
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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116 metadata field names. This is useful if a
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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117 header line is not provided with the
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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118 metadata, if you want to rename the fields,
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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119 or if you want to include only the first n
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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120 fields where n is the number of entries
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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121 provided here.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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122 --output-as-json Write the output file in JSON format.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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123 --help Show this message and exit.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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124 ]]></help>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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125 <expand macro="citations" />
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
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126 </tool>