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comparison frequency.xml @ 0:602c13b29eb5 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 08:57:25 +0000
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1 <tool id="ampvis2_frequency" name="ampvis2 frequency plot" 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 '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 library(ampvis2, quietly = TRUE)
13 data <- readRDS("$data")
14 plot <- amp_frequency(
15 data,
16 ## https://github.com/KasperSkytte/ampvis2/issues/167
17 ## #if $group_by
18 ## group_by = "$group_by",
19 ## #end if
20 ## tax_class = NULL,
21 tax_empty = "$tax_empty",
22 tax_aggregate = "$tax_aggregate",
23 weight = $weight,
24 normalise = $normalise,
25 ## TODO
26 detailed_output = FALSE
27 )
28 @OUTPUT_TOKEN@
29 ]]></configfile>
30 </configfiles>
31 <inputs>
32 <expand macro="rds_metadata_input_macro"/>
33 <!-- https://github.com/KasperSkytte/ampvis2/issues/167
34 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/> -->
35 <expand macro="tax_empty_macro"/>
36 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
37 <option value="OTU" selected="true">OTU/ASV</option>
38 </expand>
39 <param argument="weight" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the frequency by abundance"/>
40 <expand macro="normalise_macro" checked="true"/>
41 <expand macro="out_format_macro"/>
42 </inputs>
43 <outputs>
44 <expand macro="out_macro"/>
45 </outputs>
46 <tests>
47 <!-- defaults -->
48 <test expect_num_outputs="1">
49 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
50 <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf" compare="sim_size"/>
51 </test>
52 <!-- group_by -->
53 <!-- https://github.com/KasperSkytte/ampvis2/issues/167
54 <test expect_num_outputs="1">
55 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
56 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
57 <param name="group_by" value="Plant"/>
58 <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/>
59 </test> -->
60 </tests>
61 <help><![CDATA[
62 What it does
63 ============
64
65 Generates a barplot with frequency vs read abundance.
66
67 The Galaxy tool calls the `amp_frequency
68 <https://kasperskytte.github.io/ampvis2/reference/amp_frequency.html>`_ function
69 of the ampvis2 package.
70
71 Input
72 =====
73
74 @HELP_RDS_INPUT@
75
76 @HELP_METADATA_LIST_INPUT@
77
78 Output
79 ======
80
81 A frequency plot in the chosen output format.
82 ]]></help>
83 <expand macro="citations"/>
84 </tool>