Mercurial > repos > iuc > biom_add_metadata

comparison biom_add_metadata.xml @ 1:28ad7ac9c193 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
author iuc
date Wed, 11 Sep 2019 12:41:29 -0400
parents 367b1ed91207
children a3b86937ead6
comparison
equal deleted inserted replaced
0:367b1ed91207 1:28ad7ac9c193
1 <tool id="biom_add_metadata" name="BIOM metadata" version="@VERSION@.0"> 1 <tool id="biom_add_metadata" name="Add metadata" version="@VERSION@.1">
2 <description>add-metadata</description> 2 <description>to a BIOM table</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" /> 7 <expand macro="version_command" />
9 <command> 8 <command detect_errors="exit_code">
10 <![CDATA[ 9 <![CDATA[
11 biom add-metadata 10 biom add-metadata
12 -i "${input_table}" 11 --input-fp '$input_fp'
13 -o "${output_table}" 12 --output-fp '$output_fp'
14 #if $input_sample_metadata: 13 #if $sample_metadata_fp
15 --sample-metadata-fp "${input_sample_metadata}" 14 --sample-metadata-fp '$sample_metadata_fp'
16 #end if 15 #end if
17 #if $input_observation_metadata: 16 #if $observation_metadata_fp
18 --observation-metadata-fp "${input_observation_metadata}" 17 --observation-metadata-fp '$observation_metadata_fp'
19 #end if 18 #end if
20 #if $sc_separated: 19 #if $sc_separated
21 --sc-separated "${sc_separated}" 20 --sc-separated '$sc_separated'
22 #end if 21 #end if
23 #if $sc_pipe_separated: 22 #if $sc_pipe_separated
24 --sc-pipe-separated "${sc_pipe_separated}" 23 --sc-pipe-separated '$sc_pipe_separated'
25 #end if 24 #end if
26 #if $int_fields: 25 #if $int_fields
27 --int-fields "${int_fields}" 26 --int-fields '$int_fields'
28 #end if 27 #end if
29 #if $float_fields: 28 #if $float_fields
30 --float-fields "${float_fields}" 29 --float-fields '$float_fields'
31 #end if 30 #end if
32 #if $sample_header: 31 #if $sample_header
33 --sample-header "${sample_header}" 32 --sample-header '$sample_header'
34 #end if 33 #end if
35 #if $observation_header: 34 #if $observation_header
36 --observation-header "${observation_header}" 35 --observation-header '$observation_header'
37 #end if 36 #end if
38 ${output_as_json} 37 $output_as_json
39 ]]> 38 ]]>
40 </command> 39 </command>
41 <inputs> 40 <inputs>
42 <param name="input_table" type="data" format="biom1" label="BIOM File" argument="--input-fp"/> 41 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM File"/>
43 <param name="input_sample_metadata" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" argument="--sample-metadata-fp PATH"/> 42 <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Sample Metadata Tabular File" />
44 <param name="input_observation_metadata" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File" argument="--observation-metadata-fp"/> 43 <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Observation Metadata Tabular File"/>
45 <param name="sc_separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" argument="--sc-separated"/> 44 <param name="sc_separated" argument="--sc-separated" type="text" value="" label="Comma-separated list of the metadata fields to split on semicolons" />
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"/> 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 (|)"/>
47 <param name="int_fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" argument="--int-fields"/> 46 <param name="int_fields" argument="--int-fields" type="text" value="" label="Comma-separated list of the metadata fields to cast to integers" />
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"/> 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" />
49 <param name="sample_header" type="text" value="" label="Comma-separated list of the sample metadata field names" argument="--sample-header"/> 48 <param name="sample_header" argument="--sample-header" type="text" value="" label="Comma-separated list of the sample metadata field names" />
50 <param name="observation_header" type="text" value="" label="Comma-separated list of the observation metadata field names" argument="--observation-header"/> 49 <param name="observation_header" argument="--observation-header" type="text" value="" label="Comma-separated list of the observation metadata field names" />
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"/> 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)" />
52 </inputs> 51 </inputs>
53 <outputs> 52 <outputs>
54 <data format="biom1" name="output_table"> 53 <data format="biom1" name="output_fp">
55 <change_format> 54 <change_format>
56 <when input="${str( $output_as_json )}" value="" format="biom2" /> 55 <when input="${str( $output_as_json )}" value="" format="h5" />
57 </change_format> 56 </change_format>
58 </data> 57 </data>
59 </outputs> 58 </outputs>
60 <tests> 59 <tests>
61 <test> 60 <test>
62 <param name="input_table" value="input_abundance_1.biom1" ftype="biom1"/> 61 <param name="input_fp" value="input_abundance_1.biom1" ftype="biom1"/>
63 <param name="input_observation_metadata" value="input_taxonomy_1.tabular" ftype="tabular"/> 62 <param name="observation_metadata_fp" value="input_taxonomy_1.tabular" ftype="tabular"/>
64 <param name="sc_separated" value="taxonomy"/> 63 <param name="sc_separated" value="taxonomy"/>
65 <param name="input_sample_metadata"/> 64 <param name="output_as_json" value="--output-as-json"/>
66 <param name="sc_pipe_separated" value=""/> 65 <output name="output_fp" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
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> 66 </test>
74 </tests> 67 </tests>
75 <help><![CDATA[ 68 <help><![CDATA[
76 69
77 Usage: biom add-metadata [OPTIONS] 70 Usage: biom add-metadata [OPTIONS]
125 or if you want to include only the first n 118 or if you want to include only the first n
126 fields where n is the number of entries 119 fields where n is the number of entries
127 provided here. 120 provided here.
128 --output-as-json Write the output file in JSON format. 121 --output-as-json Write the output file in JSON format.
129 --help Show this message and exit. 122 --help Show this message and exit.
130
131
132 ]]></help> 123 ]]></help>
133 <expand macro="citations" /> 124 <expand macro="citations" />
134 </tool> 125 </tool>