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comparison octave.xml @ 0:b7f7d0c6d579 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 10:27:22 +0000
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children b7d443cda103
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-1:000000000000 0:b7f7d0c6d579
1 <tool id="ampvis2_octave" name="ampvis2 octave 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 '$rscript'
9 ]]></command>
10 <configfiles>
11 <configfile name="rscript"><![CDATA[
12 library(ampvis2, quietly = TRUE)
13 d <- readRDS("$data")
14 plot <- amp_octave(
15 d,
16 tax_aggregate = "$tax_aggregate",
17 #if $group_by
18 group_by = "$group_by",
19 #if $scales
20 scales = "$scales",
21 #end if
22 #end if
23 num_threads = 1
24 )
25 @OUTPUT_TOKEN@
26 ]]></configfile>
27 </configfiles>
28 <inputs>
29 <expand macro="rds_metadata_input_macro"/>
30 <expand macro="taxlevel_macro" argument="tax_aggregate" label="Aggregate (sum) OTU's to a taxonomic level initially." help="OTU's that have not been assigned at the chosen level will be removed with a message.">
31 <option value="OTU" selected="true">OTU/ASV</option>
32 </expand>
33 <expand macro="metadata_select" argument="group_by" label="Group the samples based on a metadata variable." help="Variable needs to be categorical/discrete"/>
34 <expand macro="facet_scales_macro" argument="scales" help="Only relevant if for group_by a value is selected"/>
35 <expand macro="out_format_macro"/>
36 </inputs>
37 <outputs>
38 <expand macro="out_macro"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
43 <output name="plot" value="AalborgWWTPs-octave.pdf" ftype="pdf"/>
44 </test>
45 <test>
46 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
47 <param name="tax_aggregate" value="Class"/>
48 <param name="out_format" value="png"/>
49 <output name="plot" value="AalborgWWTPs-octave.png" ftype="png"/>
50 </test>
51 <test>
52 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
53 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
54 <param name="group_by" value="Year"/>
55 <param name="scales" value="free"/>
56 <param name="out_format" value="svg"/>
57 <output name="plot" value="AalborgWWTPs-octave.svg" ftype="svg"/>
58 </test>
59 </tests>
60 <help><![CDATA[
61 What it does
62 ============
63
64 Generates an octave plot to assess alpha diversity. An octave plot is a
65 histogram of the number of taxa observed by bins of read counts, where the bin
66 ranges increase exponentially, see details.
67
68 The Galaxy tool calls the `amp_octave
69 <https://madsalbertsen.github.io/ampvis2/reference/amp_octave.html>`_ function
70 of the ampvis2 package.
71
72
73 Details
74 =======
75
76 The n-th bin in the histogram has the range ``r(n)=2n...2n+1-1``. The height of the
77 bars then reflect the number of unique taxa with read counts in each bin. By
78 judging the distribution one can assess whether the samples have been sequenced
79 deeply enough at the chosen taxonomic level. A full symmetrical bell-shaped
80 distribution with the left part far from the y-axis is the ideal. A high amount
81 of OTU's with a low amount of reads indicates noise, chimeras, and even cross
82 talk.
83
84 Aggregating OTU's using ``tax_aggregate`` is useful to assess whether the samples
85 have been sequenced deep enough to capture the full diversity at the given
86 level, but ONLY applies to OTU's that have assigned taxonomy at the given level.
87
88 It is recommended to look at samples individually as grouping samples will
89 almost always look ideal. It is better to identify "bad" samples individually
90 and remove them.
91
92 Input
93 =====
94
95 @HELP_RDS_INPUT@
96
97 @HELP_METADATA_LIST_INPUT@
98
99 Output
100 ======
101
102 Octave plot in the chosen output format.
103
104 ]]></help>
105 <expand macro="citations"/>
106 </tool>