Mercurial > repos > iuc > biom_add_metadata

annotate biom_add_metadata.xml @ 7:0b3c3ad92827 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 5fc41e15cb372b3ae635c550c387ccd41af166f7
author iuc
date Sat, 21 Jan 2023 11:16:40 +0000
parents a3b86937ead6
children 6ef0b5664c69
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
a3b86937ead6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
iuc
parents: 1
diff changeset
1 <tool id="biom_add_metadata" name="Add metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
2 <description>to a BIOM table</description>
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
3 <macros>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
4 <import>macros.xml</import>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
5 </macros>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
6 <expand macro="requirements" />
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
7 <expand macro="version_command" />
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
8 <command detect_errors="exit_code">
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
9 <![CDATA[
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
10 biom add-metadata
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
11 --input-fp '$input_fp'
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
12 --output-fp '$output_fp'
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
13 #if $sample_metadata_fp
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
14 --sample-metadata-fp '$sample_metadata_fp'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
15 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
16 #if $observation_metadata_fp
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
17 --observation-metadata-fp '$observation_metadata_fp'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
18 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
19 #if $sc_separated
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
20 --sc-separated '$sc_separated'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
21 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
22 #if $sc_pipe_separated
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
23 --sc-pipe-separated '$sc_pipe_separated'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
24 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
25 #if $int_fields
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
26 --int-fields '$int_fields'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
27 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
28 #if $float_fields
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
29 --float-fields '$float_fields'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
30 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
31 #if $sample_header
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
32 --sample-header '$sample_header'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
33 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
34 #if $observation_header
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
35 --observation-header '$observation_header'
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
36 #end if
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
37 $output_as_json
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
38 ]]>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
39 </command>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
40 <inputs>
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
41 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM File"/>
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
42 <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" />
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
43 <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File"/>
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
44 <param name="sc_separated" argument="--sc-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" />
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
45 <param name="sc_pipe_separated" argument="--sc-pipe-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)"/>
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
46 <param name="int_fields" argument="--int-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" />
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
47 <param name="float_fields" argument="--float-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" />
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
48 <param name="sample_header" argument="--sample-header" type="text" value="" label="Comma-separated list of the sample metadata field names" />
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
49 <param name="observation_header" argument="--observation-header" type="text" value="" label="Comma-separated list of the observation metadata field names" />
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
50 <param name="output_as_json" argument="--output-as-json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" />
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
51 </inputs>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
52 <outputs>
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
53 <data format="biom1" name="output_fp">
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
54 <change_format>
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
55 <when input="${str( $output_as_json )}" value="" format="h5" />
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
56 </change_format>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
57 </data>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
58 </outputs>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
59 <tests>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
60 <test>
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
61 <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/>
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
62 <param name="observation_metadata_fp" value="input_taxonomy_1.tabular" ftype="tabular"/>
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
63 <param name="sc_separated" value="taxonomy"/>
1
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
64 <param name="output_as_json" value="--output-as-json"/>
28ad7ac9c193 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
iuc
parents: 0
diff changeset
65 <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
0
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
66 </test>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
67 </tests>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
68 <help><![CDATA[
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
69
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
70 Usage: biom add-metadata [OPTIONS]
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
71
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
72 Add metadata to a BIOM table.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
73
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
74 Add sample and/or observation metadata to BIOM-formatted files. See
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
75 examples here: http://biom-format.org/documentation/adding_metadata.html
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
76
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
77 Example usage:
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
78
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
79 Add sample metadata to a BIOM table:
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
80
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
81 $ biom add-metadata -i otu_table.biom -o table_with_sample_metadata.biom
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
82 -m sample_metadata.txt
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
83
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
84 Options:
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
85 -i, --input-fp PATH The input BIOM table [required]
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
86 -o, --output-fp PATH The output BIOM table [required]
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
87 -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
iuc
parents:
diff changeset
88 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
iuc
parents:
diff changeset
89 provided).
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
90 --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
iuc
parents:
diff changeset
91 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
iuc
parents:
diff changeset
92 table, if provided).
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
93 --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
iuc
parents:
diff changeset
94 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
iuc
parents:
diff changeset
95 hierarchical data such as taxonomy or
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
96 functional categories.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
97 --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
iuc
parents:
diff changeset
98 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
iuc
parents:
diff changeset
99 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
iuc
parents:
diff changeset
100 functional categories with one-to-many
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
101 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
iuc
parents:
diff changeset
102 --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
iuc
parents:
diff changeset
103 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
iuc
parents:
diff changeset
104 integer data such as "DaysSinceStart".
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
105 --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
iuc
parents:
diff changeset
106 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
iuc
parents:
diff changeset
107 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
iuc
parents:
diff changeset
108 --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
iuc
parents:
diff changeset
109 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
iuc
parents:
diff changeset
110 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
iuc
parents:
diff changeset
111 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
iuc
parents:
diff changeset
112 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
iuc
parents:
diff changeset
113 the number of entries provided here.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
114 --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
iuc
parents:
diff changeset
115 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
iuc
parents:
diff changeset
116 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
iuc
parents:
diff changeset
117 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
iuc
parents:
diff changeset
118 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
iuc
parents:
diff changeset
119 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
iuc
parents:
diff changeset
120 provided here.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
121 --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
iuc
parents:
diff changeset
122 --help Show this message and exit.
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
123 ]]></help>
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
124 <expand macro="citations" />
367b1ed91207 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
iuc
parents:
diff changeset
125 </tool>