Mercurial > repos > iuc > ampvis2_rarecurve

comparison rarecurve.xml @ 0:65cc862ec3c4 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 10:23:15 +0000
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children 37c1c0ba406c
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-1:000000000000 0:65cc862ec3c4
1 <tool id="ampvis2_rarecurve" name="ampvis2 rarefaction curve" 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_rarecurve(
15 data,
16 stepsize = $stepsize
17 #if $color_by
18 , color_by = "$color_by",
19 #end if
20 #if $facet_by
21 , facet_by = "$facet_by",
22 #if $facet_scales
23 , facet_scales = "$facet_scales"
24 #end if
25 #end if
26 )
27
28 @OUTPUT_TOKEN@
29 ]]></configfile>
30 </configfiles>
31 <inputs>
32 <expand macro="rds_metadata_input_macro"/>
33 <!-- TODO if no metadata_list is given that the color/facet_by selects
34 give a warnings in the logs:
35 WARNI [galaxy.tools.parameters.dynamic_options] could not create dynamic options from_dataset: metadata_list not a data or collection paramete
36
37 - introduce a conditional color_facet_cond wich optionally shows these options
38 and make metadata_list required?
39 - or use a filter + proper message instead of from_datatable ?
40
41 here and everywhere else -->
42 <param argument="stepsize" type="integer" value="1000" min="1" label="Step size" help="Lower is prettier but takes more time to generate."/>
43 <expand macro="metadata_select" argument="color_by" label="Color curves by"/>
44 <expand macro="metadata_select_discrete" argument="facet_by" label="Facet curves by"/>
45 <expand macro="facet_scales_macro" argument="facet_scales" help="Only relevant if for facet_by a value is selected"/>
46 <expand macro="out_format_macro"/>
47 </inputs>
48 <outputs>
49 <expand macro="out_macro"/>
50 </outputs>
51 <tests>
52 <test>
53 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
54 <output name="plot" value="AalborgWWTPs-rarecurve.pdf" ftype="pdf"/>
55 </test>
56 <test>
57 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
58 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
59 <param name="stepsize" value="100"/>
60 <param name="color_by" value="Plant"/>
61 <output name="plot" value="AalborgWWTPs-rarecurve-color.pdf" ftype="pdf"/>
62 </test>
63 <test>
64 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
65 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
66 <param name="stepsize" value="100"/>
67 <param name="facet_by" value="Plant"/>
68 <param name="facet_scales" value="fixed"/>
69 <output name="plot" value="AalborgWWTPs-rarecurve-facet.pdf" ftype="pdf"/>
70 </test>
71 </tests>
72 <help><![CDATA[
73 What it does
74 ============
75
76 Generates a rarefaction curve (number of reads vs number of observed OTUs) for each sample.
77 The plot can be colored or faceted (i.e. split into multiple panels) by metadata
78
79 The Galaxy tool calls the `amp_rarecurve
80 <https://madsalbertsen.github.io/ampvis2/reference/amp_rarecurve.html>`_ function
81 of the ampvis2 package.
82
83 Input
84 =====
85
86 @HELP_RDS_INPUT@
87
88 @HELP_METADATA_LIST_INPUT@
89
90 Output
91 ======
92
93 Rarefaction curves in the chosen output format.
94
95 ]]></help>
96 <expand macro="citations"/>
97 </tool>