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comparison boxplot.xml @ 0:43776659edf4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author iuc
date Mon, 04 Apr 2022 10:29:47 +0000
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children de03693b75b1
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-1:000000000000 0:43776659edf4
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 ## detailed_output = TRUE
41 )
42 @OUTPUT_TOKEN@
43 ]]></configfile>
44 </configfiles>
45 <inputs>
46 <expand macro="rds_metadata_input_macro"/>
47 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples" help="by a discrete variable in the metadata"/>
48 <param argument="sort_by" type="select" label="Sort boxplots by">
49 <option value="median">Median</option>
50 <option value="mean">Mean</option>
51 <option value="total">Total</option>
52 </param>
53 <param argument="plot_type" type="select" label="Plot type">
54 <option value="boxplot">Boxplot</option>
55 <option value="point">Points</option>
56 </param>
57 <param argument="point_size" type="integer" value="1" min="0" label="Point size"/>
58 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
59 <option value="Genus" selected="true">Genus</option>
60 </expand>
61 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/>
62 <expand macro="tax_show_macro" value="20"/>
63 <expand macro="tax_empty_macro"/>
64 <param argument="plot_flip" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Flip the axes of the plot"/>
65 <param argument="plot_log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log10-scale the plot"/>
66 <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"/>
67 <expand macro="normalise_macro"/>
68 <expand macro="out_format_macro"/>
69 </inputs>
70 <outputs>
71 <expand macro="out_macro"/>
72 </outputs>
73 <tests>
74 <test>
75 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
76 <output name="plot" value="AalborgWWTPs-boxplot.pdf" ftype="pdf"/>
77 </test>
78 <test>
79 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
80 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
81 <param name="group_by" value="Plant"/>
82 <param name="sort_by" value="total"/>
83 <param name="tax_show" value="5"/>
84 <param name="plot_flip" value="true"/>
85 <param name="plot_log" value="true"/>
86 <param name="adjust_zero" value="100000"/>
87 <param name="normalise" value="true"/>
88 <output name="plot" value="AalborgWWTPs-boxplot-group.pdf" ftype="pdf"/>
89 </test>
90 <test>
91 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
92 <param name="plot_type" value="point"/>
93 <param name="point_size" value="5"/>
94 <param name="tax_aggregate" value="Order"/>
95 <param name="tax_add" value="Phylum"/>
96 <output name="plot" value="AalborgWWTPs-boxplot-point.pdf" ftype="pdf"/>
97 </test>
98 </tests>
99 <help><![CDATA[
100 What it does
101 ============
102
103 Generates boxplots of the most abundant taxa.
104
105 The Galaxy tool calls the `amp_boxplot
106 <https://madsalbertsen.github.io/ampvis2/reference/amp_boxplot.html>`_ function
107 of the ampvis2 package.
108
109 Input
110 =====
111
112 @HELP_RDS_INPUT@
113
114 @HELP_METADATA_LIST_INPUT@
115
116 Output
117 ======
118
119 Boxplot in the chosen output format.
120
121 ]]></help>
122 <expand macro="citations"/>
123 </tool>