Mercurial > repos > iuc > ampvis2_frequency

comparison frequency.xml @ 0:f77f7c426d6f 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 10:18:21 +0000
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children b8ecbc50af78
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-1:000000000000 0:f77f7c426d6f
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 #if $group_by
17 group_by = "$group_by",
18 #end if
19 ## tax_class = NULL,
20 tax_empty = "$tax_empty",
21 tax_aggregate = "$tax_aggregate",
22 weight = $weight,
23 normalise = $normalise,
24 ## TODO
25 detailed_output = FALSE
26 )
27 @OUTPUT_TOKEN@
28 ]]></configfile>
29 </configfiles>
30 <inputs>
31 <expand macro="rds_metadata_input_macro"/>
32 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by "/>
33 <expand macro="tax_empty_macro"/>
34 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
35 <option value="OTU" selected="true">OTU/ASV</option>
36 </expand>
37 <param argument="weight" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Weight the frequency by abundance"/>
38 <expand macro="normalise_macro" checked="true"/>
39 <expand macro="out_format_macro"/>
40 </inputs>
41 <outputs>
42 <expand macro="out_macro"/>
43 </outputs>
44 <tests>
45 <!-- defaults -->
46 <test expect_num_outputs="1">
47 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
48 <output name="plot" value="AalborgWWTPs-frequency.pdf" ftype="pdf"/>
49 </test>
50 <!-- group_by -->
51 <test expect_num_outputs="1">
52 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
53 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
54 <param name="group_by" value="Plant"/>
55 <output name="plot" value="AalborgWWTPs-frequency-group_by.pdf" ftype="pdf"/>
56 </test>
57 </tests>
58 <help><![CDATA[
59 What it does
60 ============
61
62 Generates a barplot with frequency vs read abundance.
63
64 The Galaxy tool calls the `amp_frequency
65 <https://madsalbertsen.github.io/ampvis2/reference/amp_frequency.html>`_ function
66 of the ampvis2 package.
67
68 Input
69 =====
70
71 @HELP_RDS_INPUT@
72
73 @HELP_METADATA_LIST_INPUT@
74
75 Output
76 ======
77
78 A frequency plot in the chosen output format.
79 ]]></help>
80 <expand macro="citations"/>
81 </tool>