Mercurial > repos > iuc > ampvis2_rankabundance

comparison rankabundance.xml @ 0:132d2a794152 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 10:20:48 +0000
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1 <tool id="ampvis2_rankabundance" name="ampvis2 rank abundance 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_rankabundance(
15 data,
16 group_by = "$group_by",
17 showSD = $showSD,
18 log10_x = $log10_x
19 )
20 @OUTPUT_TOKEN@
21 ]]></configfile>
22 </configfiles>
23 <inputs>
24 <expand macro="rds_metadata_input_macro"/>
25 <expand macro="metadata_select_discrete" argument="group_by" optional="false" label="Group the samples by"/>
26 <param argument="showSD" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Show standard deviation"/>
27 <param argument="log10_x" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Log10-transform the x-axis" help="Often most variation is observed among the most abundant OTU's, log10-transforming the x-axis will highlight this better."/>
28 <expand macro="out_format_macro"/>
29 </inputs>
30 <outputs>
31 <expand macro="out_macro"/>
32 </outputs>
33 <tests>
34 <!-- defaults -->
35 <test expect_num_outputs="1">
36 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
37 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
38 <param name="group_by" value="Plant"/>
39 <output name="plot" value="AalborgWWTPs-rankabundance.pdf" ftype="pdf"/>
40 </test>
41 <!-- non-defaults -->
42 <test expect_num_outputs="1">
43 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
44 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
45 <param name="group_by" value="Plant"/>
46 <param name="showSD" value="false"/>
47 <param name="log10_x" value="false"/>
48 <output name="plot" value="AalborgWWTPs-rankabundance-nondefault.pdf" ftype="pdf"/>
49 </test>
50 </tests>
51 <help><![CDATA[
52 What it does
53 ============
54
55 Generates a rank abundance curve (rank abundance vs cumulative read abundance),
56 optionally with standard deviation from mean intervals.
57
58 The Galaxy tool calls the `amp_rankabundance
59 <https://madsalbertsen.github.io/ampvis2/reference/amp_rankabundance.html>`_ function
60 of the ampvis2 package.
61
62 Currently only OTU level is supported.
63
64 Input
65 =====
66
67 @HELP_RDS_INPUT@
68
69 @HELP_METADATA_LIST_INPUT@
70
71 Output
72 ======
73
74 An rank abundance plot in the chosen output format.
75 ]]></help>
76 <expand macro="citations"/>
77 </tool>