Mercurial > repos > iuc > ampvis2_timeseries
comparison timeseries.xml @ 0:e77090960f62 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author | iuc |
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date | Mon, 04 Apr 2022 10:19:59 +0000 |
parents | |
children | 3c16699f39d6 |
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1 <tool id="ampvis2_timeseries" name="ampvis2 timeseries 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 #if $tax_add | |
14 #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")' | |
15 #else | |
16 #set ta='NULL' | |
17 #end if | |
18 data <- readRDS("$data") | |
19 plot <- amp_timeseries( | |
20 data, | |
21 time_variable = "$time_variable", | |
22 #if $group_by | |
23 group_by = "$group_by", | |
24 #end if | |
25 tax_aggregate = "$tax_aggregate", | |
26 tax_add = $ta, | |
27 @TAX_SHOW@ | |
28 tax_class = NULL, | |
29 tax_empty = "$tax_empty", | |
30 split = $split, | |
31 scales = "free_y", | |
32 normalise = TRUE, | |
33 plotly = FALSE, | |
34 format = "%Y-%m-%d" | |
35 ) | |
36 @OUTPUT_TOKEN@ | |
37 ]]></configfile> | |
38 </configfiles> | |
39 <inputs> | |
40 <expand macro="rds_metadata_input_macro"/> | |
41 <expand macro="metadata_select_date" argument="time_variable" optional="false" label="Time variable" help="Must be directly compatible with as_date and preferably of the form yyyy-mm-dd or %Y-%m-%d"/> | |
42 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples by"/> | |
43 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> | |
44 <option value="OTU" selected="true">OTU/ASV</option> | |
45 </expand> | |
46 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/> | |
47 <expand macro="tax_show_macro" value="6"/> | |
48 <expand macro="tax_empty_macro"/> | |
49 <param argument="split" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Create a facet for each taxon"/> | |
50 <expand macro="facet_scales_macro" argument="scales"/> | |
51 <expand macro="normalise_macro" checked="true"/> | |
52 <expand macro="out_format_macro"/> | |
53 </inputs> | |
54 <outputs> | |
55 <expand macro="out_macro"/> | |
56 </outputs> | |
57 <tests> | |
58 <!-- defaults --> | |
59 <test expect_num_outputs="1"> | |
60 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | |
61 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | |
62 <param name="time_variable" value="Date"/> | |
63 <output name="plot" value="AalborgWWTPs-timeseries.pdf" ftype="pdf"/> | |
64 </test> | |
65 <!-- group --> | |
66 <test expect_num_outputs="1"> | |
67 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | |
68 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | |
69 <param name="time_variable" value="Date"/> | |
70 <param name="group_by" value="Plant"/> | |
71 <output name="plot" value="AalborgWWTPs-timeseries-group.pdf" ftype="pdf"/> | |
72 </test> | |
73 <!-- taxlevel --> | |
74 <test expect_num_outputs="1"> | |
75 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | |
76 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | |
77 <param name="time_variable" value="Date"/> | |
78 <param name="tax_aggregate" value="Family"/> | |
79 <param name="tax_add" value="Phylum"/> | |
80 <output name="plot" value="AalborgWWTPs-timeseries-tax.pdf" ftype="pdf"/> | |
81 </test> | |
82 </tests> | |
83 <help><![CDATA[ | |
84 What it does | |
85 ============ | |
86 | |
87 Generates a timeseries plot showing relative read abundances over time. | |
88 | |
89 The Galaxy tool calls the `amp_timeseries | |
90 <https://madsalbertsen.github.io/ampvis2/reference/amp_timeseries.html>`_ function | |
91 of the ampvis2 package. | |
92 | |
93 @HELP_RELATIVE_ABUNDANCES@ | |
94 | |
95 Input | |
96 ===== | |
97 | |
98 @HELP_RDS_INPUT@ | |
99 | |
100 @HELP_METADATA_LIST_INPUT@ | |
101 | |
102 Output | |
103 ====== | |
104 | |
105 A timeseries plot in the chosen output format. | |
106 | |
107 ]]></help> | |
108 <expand macro="citations"/> | |
109 </tool> |