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comparison setmetadata.xml @ 0:e4e8e349c2c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author iuc
date Fri, 16 Aug 2024 08:55:07 +0000
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1 <tool id="ampvis2_setmetadata" name="ampvis2 set metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>types</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="header"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 library(lubridate, quietly = TRUE)
13 data <- readRDS("$data")
14 #for col in $numbers
15 data\$metadata\$$col <- as.numeric(data\$metadata\$$col)
16 #end for
17 #for col in $integers
18 data\$metadata\$$col <- as.integer(data\$metadata\$$col)
19 #end for
20 #for col in $dates
21 data\$metadata\$$col <- as_date(data\$metadata\$$col)
22 #end for
23 saveRDS(data, "$ampvis")
24 @SAVE_METADATA_LIST@
25 ]]></configfile>
26 </configfiles>
27 <inputs>
28 <expand macro="rds_metadata_input_macro" metadata_optional="false"/>
29 <expand macro="metadata_select" an="name" argument="character" multiple="true" label="Character metadata variables"/>
30 <expand macro="metadata_select" an="name" argument="numbers" multiple="true" label="Numerical metadata variables">
31 <token name="options">
32 <filter type="param_value" column="0" ref="character" keep="false"/>
33 </token>
34 </expand>
35 <expand macro="metadata_select" an="name" argument="integers" multiple="true" label="Discrete numerical metadata variables (integers)">
36 <token name="options">
37 <filter type="param_value" column="0" ref="character" keep="false"/>
38 <filter type="param_value" column="0" ref="numbers" keep="false"/>
39 </token>
40 </expand>
41 <expand macro="metadata_select" an="name" argument="dates" multiple="true" label="Date metadata variables">
42 <token name="options">
43 <filter type="param_value" column="0" ref="character" keep="false"/>
44 <filter type="param_value" column="0" ref="numbers" keep="false"/>
45 <filter type="param_value" column="0" ref="integers" keep="false"/>
46 </token>
47 </expand>
48 </inputs>
49 <outputs>
50 <data name="ampvis" format="ampvis2"/>
51 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
52 </outputs>
53 <tests>
54 <!-- -->
55 <test expect_num_outputs="2">
56 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
57 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
58 <param name="numbers" value="Year"/>
59 <param name="dates" value="Date"/>
60 <output name="ampvis" ftype="ampvis2">
61 <assert_contents>
62 <has_size value="11966" delta="1000"/>
63 </assert_contents>
64 </output>
65 </test>
66 </tests>
67 <help><![CDATA[
68 What it does
69 ============
70
71 Allows to manually set the data types of metadata. `ampvis2: load` tries to
72 detect the metadata data types automatically. If this is not as desired
73 the data types can be set manually with this tool.
74
75 Input
76 =====
77
78 @HELP_RDS_INPUT@
79
80 @HELP_METADATA_LIST_INPUT@
81
82 Output
83 ======
84
85 **RDS**
86
87 The main output of the tool is an RDS data set that contains the R representation of
88 the ampvis2 object containing the same data as the input, but with data types changes
89 as chosen in the input form.
90
91 **Metadata list file**
92
93 Updated metadata (only column 4 should change and reflect the desired datatype changes).
94 ]]></help>
95 <expand macro="citations"/>
96 </tool>