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comparison boxplot.xml @ 0:797603efc62d 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 08:50:10 +0000
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1 <tool id="ampvis2_boxplot" name="ampvis2 boxplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description></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 #if $tax_add
13 #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")'
14 #else
15 #set ta='NULL'
16 #end if
17 library(ampvis2, quietly = TRUE)
18 d <- readRDS("$data")
19 plot <- amp_boxplot(
20 d,
21 #if $group_by
22 group_by = "$group_by",
23 #end if
24 sort_by = "$sort_by",
25 plot_type = "$plot_type",
26 point_size = $point_size,
27 tax_aggregate = "$tax_aggregate",
28 tax_add = $ta,
29 @TAX_SHOW@
30 tax_empty = "$tax_empty",
31 ## tax_class = NULL,
32 ## order_group = NULL,
33 ## order_y = NULL,
34 plot_flip = $plot_flip,
35 plot_log = $plot_log,
36 #if str($adjust_zero) != ""
37 adjust_zero = $adjust_zero,
38 #end if
39 normalise = $normalise
40 )
41 @OUTPUT_TOKEN@
42 ]]></configfile>
43 </configfiles>
44 <inputs>
45 <expand macro="rds_metadata_input_macro"/>
46 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples" help="by a discrete variable in the metadata"/>
47 <param argument="sort_by" type="select" label="Sort boxplots by">
48 <option value="median">Median</option>
49 <option value="mean">Mean</option>
50 <option value="sum">Sum</option>
51 </param>
52 <param argument="plot_type" type="select" label="Plot type">
53 <option value="boxplot">Boxplot</option>
54 <option value="point">Points</option>
55 </param>
56 <param argument="point_size" type="integer" value="1" min="0" label="Point size"/>
57 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
58 <option value="Genus" selected="true">Genus</option>
59 </expand>
60 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/>
61 <expand macro="tax_show_macro" value="20"/>
62 <expand macro="tax_empty_macro"/>
63 <param argument="plot_flip" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Flip the axes of the plot"/>
64 <param argument="plot_log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log10-scale the plot"/>
65 <param argument="adjust_zero" type="integer" value="" min="1" optional="true" label="Add value to abundances" help="in order to keep abundances of 0 in the calculation of medians"/>
66 <expand macro="normalise_macro"/>
67 <expand macro="out_format_macro"/>
68 </inputs>
69 <outputs>
70 <expand macro="out_macro"/>
71 </outputs>
72 <tests>
73 <test>
74 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
75 <output name="plot" value="AalborgWWTPs-boxplot.pdf" ftype="pdf" compare="sim_size"/>
76 </test>
77 <test>
78 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
79 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
80 <param name="group_by" value="Plant"/>
81 <param name="sort_by" value="sum"/>
82 <param name="tax_show" value="5"/>
83 <param name="plot_flip" value="true"/>
84 <param name="plot_log" value="true"/>
85 <param name="adjust_zero" value="100000"/>
86 <param name="normalise" value="true"/>
87 <output name="plot" value="AalborgWWTPs-boxplot-group.pdf" ftype="pdf" compare="sim_size"/>
88 </test>
89 <test>
90 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
91 <param name="plot_type" value="point"/>
92 <param name="point_size" value="5"/>
93 <param name="tax_aggregate" value="Order"/>
94 <param name="tax_add" value="Phylum"/>
95 <output name="plot" value="AalborgWWTPs-boxplot-point.pdf" ftype="pdf" compare="sim_size"/>
96 </test>
97 </tests>
98 <help><![CDATA[
99 What it does
100 ============
101
102 Generates boxplots of the most abundant taxa.
103
104 The Galaxy tool calls the `amp_boxplot
105 <https://kasperskytte.github.io/ampvis2/reference/amp_boxplot.html>`_ function
106 of the ampvis2 package.
107
108 Input
109 =====
110
111 @HELP_RDS_INPUT@
112
113 @HELP_METADATA_LIST_INPUT@
114
115 Output
116 ======
117
118 Boxplot in the chosen output format.
119
120 ]]></help>
121 <expand macro="citations"/>
122 </tool>