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comparison subset_samples.xml @ 0:1187994f81a2 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 08:53:18 +0000
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1 <tool id="ampvis2_subset_samples" name="ampvis2 subset samples" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>by sample metadata</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="header"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 library(ampvis2, quietly = TRUE)
13 data <- readRDS("$data")
14 #set vals = 'c("' + '", "'.join(str($vals).split(",")) + '")'
15 data <- amp_subset_samples(
16 data,
17 $invert $var %in% $vals,
18 minreads = $minreads
19 @RAREFY_TOKEN@,
20 normalise = $normalise,
21 removeAbsents = $removeAbsents
22 )
23 saveRDS(data, "$ampvis")
24 @SAVE_METADATA_LIST@
25 ]]></configfile>
26 </configfiles>
27 <inputs>
28 <expand macro="rds_metadata_input_macro"/>
29 <expand macro="metadata_select" an="name" argument="var" optional="false" multiple="false" label="Metadata variable"/>
30 <param name="vals" type="select" optional="false" multiple="true" label="Metadata value(s)">
31 <options from_dataset="metadata_list">
32 <column name="name" index="1"/>
33 <column name="value" index="1"/>
34 <filter type="param_value" ref="var" column="0"/>
35 <filter type="unique_value" column="1"/>
36 </options>
37 </param>
38 <param name="invert" type="boolean" truevalue="!" falsevalue="" checked="false"/>
39 <param argument="minreads" type="integer" value="0" min="0" label="Minimum number of reads" help="Per sample. Samples below this value will be removed initially"/>
40 <expand macro="rarefy_macro" help="This is done initially, but after filtering based on the minreads value, if set."/>
41 <expand macro="normalise_macro"/>
42 <param argument="removeAbsents" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"/>
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 <!-- defaults -->
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="var" value="Plant"/>
54 <param name="vals" value="Aalborg East"/>
55 <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
56 <output name="metadata_list_out" ftype="tabular">
57 <assert_contents>
58 <has_line line="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
59 <not_has_text text="Plant&#9;Aalborg West&#9;FALSE&#9;character"/>
60 <has_n_lines n="85"/>
61 <has_n_columns n="4"/>
62 </assert_contents>
63 </output>
64 </test>
65 <!-- test NA values in metadata -->
66 <test expect_num_outputs="2">
67 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
68 <param name="metadata_list" value="AalborgWWTPs-metadata_NA.list"/>
69 <param name="var" value="Plant"/>
70 <param name="vals" value="Aalborg East"/>
71 <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
72 <output name="metadata_list_out" ftype="tabular">
73 <assert_contents>
74 <has_line line="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
75 <not_has_text text="SampleID&#9;NA&#9;TRUE&#9;character"/>
76 <has_n_lines n="85"/>
77 <has_n_columns n="4"/>
78 </assert_contents>
79 </output>
80 </test>
81 <!-- invert -->
82 <test expect_num_outputs="2">
83 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
84 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
85 <param name="var" value="Plant"/>
86 <param name="vals" value="Aalborg East"/>
87 <param name="invert" value="true"/>
88 <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
89 <output name="metadata_list_out" ftype="tabular">
90 <assert_contents>
91 <not_has_text text="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
92 <has_line line="Plant&#9;Aalborg West&#9;FALSE&#9;character"/>
93 <has_n_lines n="79"/>
94 <has_n_columns n="4"/>
95 </assert_contents>
96 </output>
97 </test>
98 </tests>
99 <help><![CDATA[
100 What it does
101 ============
102
103 Subsets the data in ampvis2 objects based on metadata and returns the subsetted object.
104
105 The Galaxy tool calls the `amp_subset_samples
106 <https://kasperskytte.github.io/ampvis2/reference/amp_filter_samples.html>`_ function
107 of the ampvis2 package.
108
109 The subset is performed on the metadata by ``subset()`` and the abundance- and taxonomy
110 tables are then adjusted accordingly.
111
112 @HELP_RELATIVE_ABUNDANCES@
113
114 Input
115 =====
116
117 @HELP_RDS_INPUT@
118
119 @HELP_METADATA_LIST_INPUT@
120
121 Output
122 ======
123
124 An ampvis2_rds dataset containing subsetted data and an updated metadata list dataset.
125
126 ]]></help>
127 <expand macro="citations"/>
128 </tool>