Mercurial > repos > iuc > ampvis2_otu_network
comparison otu_network.xml @ 0:4bcb464fb3f3 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 10:24:03 +0000 |
parents | |
children | f8c8c943245f |
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1 <tool id="ampvis2_otu_network" name="ampvis2 OTU network 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_otu_network( | |
20 data, | |
21 min_abundance = $min_abundance, | |
22 #if $color_by | |
23 color_by = "$color_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 normalise = $normalise, | |
31 ## TODO | |
32 detailed_output = FALSE, | |
33 ) | |
34 @OUTPUT_TOKEN@ | |
35 ]]></configfile> | |
36 </configfiles> | |
37 <inputs> | |
38 <expand macro="rds_metadata_input_macro"/> | |
39 <param argument="min_abundance" type="float" value="0" min="0" label="Minimum taxa abundance" help="per sample"/> | |
40 <expand macro="metadata_select" argument="color_by" label="Color the samples by"/> | |
41 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs"> | |
42 <option value="Phylum" selected="true">Phylum</option> | |
43 </expand> | |
44 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/> | |
45 <expand macro="tax_show_macro" value="10"/> | |
46 <expand macro="tax_empty_macro"/> | |
47 <expand macro="normalise_macro" checked="true"/> | |
48 <expand macro="out_format_macro"/> | |
49 </inputs> | |
50 <outputs> | |
51 <expand macro="out_macro"/> | |
52 </outputs> | |
53 <tests> | |
54 <!-- defaults --> | |
55 <test expect_num_outputs="1"> | |
56 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | |
57 <output name="plot" value="AalborgWWTPs-otu_network.pdf" ftype="pdf" compare="sim_size"/> | |
58 </test> | |
59 <!-- defaults color --> | |
60 <test expect_num_outputs="1"> | |
61 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | |
62 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | |
63 <param name="color_by" value="Plant"/> | |
64 <output name="plot" value="AalborgWWTPs-otu_network-color_by.pdf" ftype="pdf" compare="sim_size"/> | |
65 </test> | |
66 </tests> | |
67 <help><![CDATA[ | |
68 What it does | |
69 ============ | |
70 | |
71 Generates network plot of taxa and samples. | |
72 | |
73 The Galaxy tool calls the `amp_otu_network | |
74 <https://madsalbertsen.github.io/ampvis2/reference/amp_otu_network.html>`_ function | |
75 of the ampvis2 package (based on ggnet2.). | |
76 | |
77 Input | |
78 ===== | |
79 | |
80 @HELP_RDS_INPUT@ | |
81 | |
82 @HELP_METADATA_LIST_INPUT@ | |
83 | |
84 Output | |
85 ====== | |
86 | |
87 An OTU network plot in the chosen output format. | |
88 ]]></help> | |
89 <expand macro="citations"/> | |
90 </tool> |