Mercurial > repos > iuc > ampvis2_venn

comparison venn.xml @ 0:11d29b7b44f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author iuc
date Fri, 16 Aug 2024 08:55:39 +0000
parents
children c8999971bab3
comparison
equal deleted inserted replaced
-1:000000000000 0:11d29b7b44f9
1 <tool id="ampvis2_venn" name="ampvis2 venn diagram" 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_venn(
15 data,
16 #if $group_by
17 group_by = "$group_by",
18 #end if
19 cut_a = $cut_a,
20 cut_f = $cut_f,
21 text_size = $text_size,
22 normalise = $normalise,
23 ## detailed_output = TRUE seems not supported yet https://github.com/MadsAlbertsen/ampvis2/issues/132
24 )
25 ## names(plot)
26 @OUTPUT_TOKEN@
27 ]]></configfile>
28 </configfiles>
29 <inputs>
30 <expand macro="rds_metadata_input_macro"/>
31 <expand macro="metadata_select_discrete" argument="group_by" label="Group the data by" halp="Currently only supports a maximum of 3 different groups.">
32 <validator type="expression" message="A maximum of 3 different groups is supported"><![CDATA[len(str(value).split(",")) < 4]]></validator>
33 </expand>
34 <param argument="cut_a" type="float" value="0.1" min="0" max="100" label="Abundance cutoff (percent)" help="OTU's below this abundance are excluded from the analysis"/>
35 <param argument="cut_f" type="float" value="80" min="0" max="100" label="Frequency cutoff (percent)" help="OTU's within the top cut_f of the reads are considered a core OTU"/>
36 <param argument="text_size" type="integer" value="5" min="1" label="Size of the plotted text."/>
37 <expand macro="normalise_macro"/>
38 <expand macro="out_format_macro"/>
39 </inputs>
40 <outputs>
41 <expand macro="out_macro"/>
42 </outputs>
43 <tests>
44 <!-- defaults -->
45 <test expect_num_outputs="1">
46 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
47 <output name="plot" value="AalborgWWTPs-venn.pdf" ftype="pdf" compare="sim_size"/>
48 </test>
49 <!-- defaults + group_by -->
50 <test expect_num_outputs="1">
51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
52 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
53 <param name="group_by" value="Plant"/>
54 <output name="plot" value="AalborgWWTPs-venn-group.pdf" ftype="pdf" compare="sim_size"/>
55 </test>
56 </tests>
57 <help><![CDATA[
58 What it does
59 ============
60
61 Calculates the number of "core" OTUs shared by groups given thresholds for how
62 frequent the OTUs should be above a certain abundance. Also returns the average
63 abundance of the OTUs in a particular group.
64
65 The Galaxy tool calls the `amp_venn
66 <https://kasperskytte.github.io/ampvis2/reference/amp_venn.html>`_ function
67 of the ampvis2 package.
68
69 @HELP_RELATIVE_ABUNDANCES@
70
71 Input
72 =====
73
74 @HELP_RDS_INPUT@
75
76 @HELP_METADATA_LIST_INPUT@
77
78 Output
79 ======
80
81 A venn diagram in the chosen output format.
82 ]]></help>
83 <expand macro="citations"/>
84 </tool>