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comparison biom_add_metadata.xml @ 0:367b1ed91207 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
author iuc
date Tue, 07 Jun 2016 17:25:44 -0400
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children 28ad7ac9c193
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1 <tool id="biom_add_metadata" name="BIOM metadata" version="@VERSION@.0">
2 <description>add-metadata</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command>
10 <![CDATA[
11 biom add-metadata
12 -i "${input_table}"
13 -o "${output_table}"
14 #if $input_sample_metadata:
15 --sample-metadata-fp "${input_sample_metadata}"
16 #end if
17 #if $input_observation_metadata:
18 --observation-metadata-fp "${input_observation_metadata}"
19 #end if
20 #if $sc_separated:
21 --sc-separated "${sc_separated}"
22 #end if
23 #if $sc_pipe_separated:
24 --sc-pipe-separated "${sc_pipe_separated}"
25 #end if
26 #if $int_fields:
27 --int-fields "${int_fields}"
28 #end if
29 #if $float_fields:
30 --float-fields "${float_fields}"
31 #end if
32 #if $sample_header:
33 --sample-header "${sample_header}"
34 #end if
35 #if $observation_header:
36 --observation-header "${observation_header}"
37 #end if
38 ${output_as_json}
39 ]]>
40 </command>
41 <inputs>
42 <param name="input_table" type="data" format="biom1" label="BIOM File" argument="--input-fp"/>
43 <param name="input_sample_metadata" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" argument="--sample-metadata-fp PATH"/>
44 <param name="input_observation_metadata" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File" argument="--observation-metadata-fp"/>
45 <param name="sc_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" argument="--sc-separated"/>
46 <param name="sc_pipe_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons and pipes (|)" argument="--sc-pipe-separated"/>
47 <param name="int_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" argument="--int-fields"/>
48 <param name="float_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to floating point numbers" argument="--float-fields"/>
49 <param name="sample_header" type="text" value="" label="Comma-separated list of the sample metadata field names" argument="--sample-header"/>
50 <param name="observation_header" type="text" value="" label="Comma-separated list of the observation metadata field names" argument="--observation-header"/>
51 <param name="output_as_json" type="boolean" checked="True" truevalue="--output-as-json" falsevalue="" label="Write the output file in JSON format (biom1)" argument="--output-as-json"/>
52 </inputs>
53 <outputs>
54 <data format="biom1" name="output_table">
55 <change_format>
56 <when input="${str( $output_as_json )}" value="" format="biom2" />
57 </change_format>
58 </data>
59 </outputs>
60 <tests>
61 <test>
62 <param name="input_table" value="input_abundance_1.biom1" ftype="biom1"/>
63 <param name="input_observation_metadata" value="input_taxonomy_1.tabular" ftype="tabular"/>
64 <param name="sc_separated" value="taxonomy"/>
65 <param name="input_sample_metadata"/>
66 <param name="sc_pipe_separated" value=""/>
67 <param name="int_fields" value=""/>
68 <param name="float_fields" value=""/>
69 <param name="sample_header" value=""/>
70 <param name="observation_header" value=""/>
71 <param name="output_as_json" value="True"/>
72 <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
73 </test>
74 </tests>
75 <help><![CDATA[
76
77 Usage: biom add-metadata [OPTIONS]
78
79 Add metadata to a BIOM table.
80
81 Add sample and/or observation metadata to BIOM-formatted files. See
82 examples here: http://biom-format.org/documentation/adding_metadata.html
83
84 Example usage:
85
86 Add sample metadata to a BIOM table:
87
88 $ biom add-metadata -i otu_table.biom -o table_with_sample_metadata.biom
89 -m sample_metadata.txt
90
91 Options:
92 -i, --input-fp PATH The input BIOM table [required]
93 -o, --output-fp PATH The output BIOM table [required]
94 -m, --sample-metadata-fp PATH The sample metadata mapping file (will add
95 sample metadata to the input BIOM table, if
96 provided).
97 --observation-metadata-fp PATH The observation metadata mapping file (will
98 add observation metadata to the input BIOM
99 table, if provided).
100 --sc-separated TEXT Comma-separated list of the metadata fields
101 to split on semicolons. This is useful for
102 hierarchical data such as taxonomy or
103 functional categories.
104 --sc-pipe-separated TEXT Comma-separated list of the metadata fields
105 to split on semicolons and pipes ("|"). This
106 is useful for hierarchical data such as
107 functional categories with one-to-many
108 mappings (e.g. x;y;z|x;y;w)).
109 --int-fields TEXT Comma-separated list of the metadata fields
110 to cast to integers. This is useful for
111 integer data such as "DaysSinceStart".
112 --float-fields TEXT Comma-separated list of the metadata fields
113 to cast to floating point numbers. This is
114 useful for real number data such as "pH".
115 --sample-header TEXT Comma-separated list of the sample metadata
116 field names. This is useful if a header line
117 is not provided with the metadata, if you
118 want to rename the fields, or if you want to
119 include only the first n fields where n is
120 the number of entries provided here.
121 --observation-header TEXT Comma-separated list of the observation
122 metadata field names. This is useful if a
123 header line is not provided with the
124 metadata, if you want to rename the fields,
125 or if you want to include only the first n
126 fields where n is the number of entries
127 provided here.
128 --output-as-json Write the output file in JSON format.
129 --help Show this message and exit.
130
131
132 ]]></help>
133 <expand macro="citations" />
134 </tool>