Mercurial > repos > iuc > ampvis2_alpha_diversity

annotate alpha_diversity.xml @ 8:77000428c613 draft default tip

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 cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
author iuc
date Fri, 01 Nov 2024 17:09:34 +0000
parents 289d6299bd2e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
1 <tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
2 <description></description>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
3 <macros>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
5 </macros>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
6 <expand macro="header"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
8 Rscript '$rscript'
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
9 ]]></command>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
10 <configfiles>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
11 <configfile name="rscript"><![CDATA[
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
12 #set m='"' + '", "'.join(str($measure).split(",")) + '"'
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
13 library(ampvis2, quietly = TRUE)
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
14
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
15 d <- readRDS("$data")
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
16 table <- amp_alphadiv(d,
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
17 measure = c($m),
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
18 richness = $richness
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
19 @RAREFY_TOKEN@,
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
20 )
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
21 plot <- amp_alphadiv(d,
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
22 measure = c($m),
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
23 richness = $richness
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
24 @RAREFY_TOKEN@,
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
25 plot = TRUE,
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
26 plot_group_by = "$group_by",
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
27 plot_scatter = $plot_scatter
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
28 )
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
29 write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE)
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
30 ggsave("$alphadiv_plot",
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
31 plot = plot,
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
32 device = "$output_options.out_format"
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
33 #if str($output_options.plot_width) != ''
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
34 , width = $output_options.plot_width
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
35 #end if
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
36 #if str($output_options.plot_height) != ''
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
37 , height = $output_options.plot_height
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
38 #end if
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
39 )
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
40 ]]></configfile>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
41 </configfiles>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
42 <inputs>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
43 <expand macro="rds_input_macro"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
44 <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included">
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
45 <option value="observed" selected="true">observed</option>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
46 <option value="shannon" selected="true">shannon</option>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
47 <option value="simpson" selected="true">simpson</option>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
48 <option value="invsimpson" selected="true">invsimpson</option>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
49 </param>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
50 <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
51 <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/>
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
52 <param argument="group_by" type="text" label="Group by metadata field (for plotting)" help="Specify the metadata field to group the plot by"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
53 <param argument="plot_scatter" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scatter plot instead of boxplot?" help="Select to generate a scatter plot instead of a boxplot"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
54 <expand macro="out_format_macro"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
55 </inputs>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
56 <outputs>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
57 <data name="alphadiv" format="tabular"/>
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
58 <expand macro="out_macro" name="alphadiv_plot" label=": plot"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
59 </outputs>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
60 <tests>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
61 <test>
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
62 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
63 <param name="group_by" value="Plant"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
64 <param name="plot_scatter" value="false"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
65 <output name="alphadiv">
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
66 <assert_contents>
6
289d6299bd2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb30e4b8d695e096753fe7cb5056b118b25a87fd
iuc
parents: 2
diff changeset
67 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
68 <has_text text="16SAMP-536&#9;"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
69 <has_text text="&#9;Aalborg West&#9;"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
70 <has_n_lines n="68"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
71 <has_n_columns n="10"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
72 </assert_contents>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
73 </output>
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
74 <output name="alphadiv_plot" ftype="pdf">
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
75 <assert_contents>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
76 <has_size min="1"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
77 </assert_contents>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
78 </output>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
79 </test>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
80 <test>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
81 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
82 <param name="measure" value="observed,shannon"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
83 <param name="richness" value="true"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
84 <param name="rarefy" value="500"/>
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
85 <param name="group_by" value="Plant"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
86 <param name="plot_scatter" value="true"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
87 <output name="alphadiv">
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
88 <assert_contents>
6
289d6299bd2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb30e4b8d695e096753fe7cb5056b118b25a87fd
iuc
parents: 2
diff changeset
89 <has_line line="SampleID&#9;Plant&#9;Date&#9;Year&#9;Period&#9;RawReads&#9;Reads&#9;uniqueOTUs&#9;Shannon&#9;Simpson&#9;invSimpson&#9;Chao1&#9;ACE"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
90 <has_text text="16SAMP-536&#9;"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
91 <has_text text="&#9;Aalborg West&#9;"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
92 <has_n_lines n="68"/>
6
289d6299bd2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb30e4b8d695e096753fe7cb5056b118b25a87fd
iuc
parents: 2
diff changeset
93 <has_n_columns n="13"/>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
94 <has_text text="&#9;500&#9;"/>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
95 </assert_contents>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
96 </output>
8
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
97 <output name="alphadiv_plot">
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
98 <assert_contents>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
99 <has_size min="1"/>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
100 </assert_contents>
77000428c613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
iuc
parents: 6
diff changeset
101 </output>
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
102 </test>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
103 </tests>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
104 <help><![CDATA[
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
105
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
106 What it does
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
107 ============
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
108
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
109 Calculate alpha-diversity indices for each sample and combines with the metadata.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
110
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
111 The Galaxy tool calls the `amp_alpha_diversity
2
21b85417e4c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
iuc
parents: 0
diff changeset
112 <https://kasperskytte.github.io/ampvis2/reference/amp_alphadiv.html>`_ function
0
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
113 of the ampvis2 package.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
114
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
115 Usage
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
116 =====
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
117
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
118 The alpha-diversity indices are calculated per sample using the vegan function `diversity <https://rdrr.io/pkg/vegan/man/diversity.html>`_,
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
119 where the read abundances are first rarefied using `rrarefy <https://rdrr.io/pkg/vegan/man/rarefy.html>`_ by the size of the rarefy argument.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
120 Refer to the vegan documentation for details about the different indices and how they are
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
121 calculated.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
122
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
123
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
124 Input
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
125 =====
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
126
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
127 @HELP_RDS_INPUT@
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
128
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
129 Output
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
130 ======
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
131
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
132 A tabular dataset containing the chosen alpha-diversity measures per sample.
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
133
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
134 ]]></help>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
135 <expand macro="citations">
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
136 <citation type="doi">10.1371/journal.pcbi.1003531</citation>
b54f72135f58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
137 </expand>
6
289d6299bd2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb30e4b8d695e096753fe7cb5056b118b25a87fd
iuc
parents: 2
diff changeset
138 </tool>