Mercurial > repos > iuc > ampvis2_setmetadata

comparison setmetadata.xml @ 0:7499e3a586c0 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/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author iuc
date Mon, 04 Apr 2022 10:30:36 +0000
parents
children 20a46ce12854
comparison
equal deleted inserted replaced
-1:000000000000 0:7499e3a586c0
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_datetime(data\$metadata\$$col)
22 #end for
23 saveRDS(data, "$ampvis")
24 @SAVE_METADATA_LIST@
25 ]]></configfile>
26 </configfiles>
27 <inputs>
28 <expand macro="rds_metadata_input_macro" metadata_optional="false"/>
29 <expand macro="metadata_select" an="name" argument="character" multiple="true" label="Character metadata variables">
30 </expand>
31 <expand macro="metadata_select" an="name" argument="numbers" multiple="true" label="Numerical metadata variables">
32 <filter type="param_value" column="0" ref="character" keep="false"/>
33 </expand>
34 <expand macro="metadata_select" an="name" argument="integers" multiple="true" label="Discrete numerical metadata variables (integers)">
35 <filter type="param_value" column="0" ref="character" keep="false"/>
36 <filter type="param_value" column="0" ref="numbers" keep="false"/>
37 </expand>
38 <expand macro="metadata_select" an="name" argument="dates" multiple="true" label="Date metadata variables">
39 <filter type="param_value" column="0" ref="character" keep="false"/>
40 <filter type="param_value" column="0" ref="numbers" keep="false"/>
41 <filter type="param_value" column="0" ref="integers" keep="false"/>
42 </expand>
43 </inputs>
44 <outputs>
45 <data name="ampvis" format="ampvis2"/>
46 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
47 </outputs>
48 <tests>
49 <!-- -->
50 <test expect_num_outputs="2">
51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
52 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
53 <param name="numbers" value="Year"/>
54 <param name="dates" value="Date"/>
55 <output name="ampvis" ftype="ampvis2">
56 <assert_contents>
57 <has_size value="11966" delta="1000"/>
58 </assert_contents>
59 </output>
60 </test>
61 </tests>
62 <help><![CDATA[
63 What it does
64 ============
65
66 Allows to manually set the data types of metadata. `ampvis2: load` tries to
67 detect the metadata data types automatically. If this is not as desired
68 the data types can be set manually with this tool.
69
70 Input
71 =====
72
73 @HELP_RDS_INPUT@
74
75 @HELP_METADATA_LIST_INPUT@
76
77 Output
78 ======
79
80 **RDS**
81
82 The main output of the tool is an RDS data set that contains the R representation of
83 the ampvis2 object containing the same data as the input, but with data types changes
84 as chosen in the input form.
85
86 **Metadata list file**
87
88 Updated metadata (only column 4 should change and reflect the desired datatype changes).
89 ]]></help>
90 <expand macro="citations"/>
91 </tool>