Mercurial > repos > qfabrepo > metadegalaxy_symmetric_plot

comparison symmetric_plot.xml @ 0:0cac08094b86 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/symmetric_plot commit a68579d7bdde7420b8f04346d3b6e361588acf50"
author qfabrepo
date Mon, 14 Sep 2020 06:04:44 +0000
parents
children 680917d9d415
comparison
equal deleted inserted replaced
-1:000000000000 0:0cac08094b86
1 <tool id="symmetricPlot" name="Symmetric Plot" version="1.0.1" hidden="false" force_history_refresh="True">>
2 <description>Symmetric Plot</description>
3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
6 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="0.6.3">r-tidyr</requirement>
9 <requirement type="package" version="9.18">ghostscript</requirement>
10 <tool id="symmetricPlot2" name="Symmetric Plot" version="1.0.1" hidden="false" force_history_refresh="True">>
11 <description>Symmetric Plot</description>
12 <requirements>
13 <requirement type="package" version="3.4.1">r-base</requirement>
14 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
15 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
16 <requirement type="package" version="1.20.0">r-getopt</requirement>
17 <requirement type="package" version="0.6.3">r-tidyr</requirement>
18 <requirement type="package" version="9.18">ghostscript</requirement>
19 </requirements>
20 <version_command><![CDATA[
21 echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
22 ]]></version_command>
23 <command detect_errors="exit_code"><![CDATA[
24 Rscript '${__tool_directory__}/symmetric_plot.r'
25 --input.data='$input_table'
26 --meta.data='$meta_table'
27 --obs.data='$obs_table'
28 --taxrank='$taxonomy_rank'
29 --record='$nTop'
30 --norm="${norm_bool}"
31 --n.column="${selectedCol}"
32 --g.group="${group}"
33 --outdir="$htmlfile.files_path"
34 --htmlfile='$htmlfile'
35 ]]></command>
36
37 <inputs>
38 <param format="tabular" name="input_table" type="data" label="Count table file"/>
39 <param format="tabular" name="meta_table" type="data" label="Metadata file"/>
40 <param format="tabular" name="obs_table" type="data" label="OTU Taxonomy file"/>
41
42 <param name="nTop" type="select" display="radio" label="Select number of records to display">
43 <option value="20" selected="true">20</option>
44 <option value="30">30</option>
45 <option value="40">40</option>
46 <option value="50">50</option>
47 <option value="100">100</option>
48 </param>
49
50 <param name="taxonomy_rank" type="select" display="radio" label="Select a taxonomy rank">
51 <option value="Kingdom" selected="true">Kingdom</option>
52 <option value="Phylum">Phylum</option>
53 <option value="Class">Class</option>
54 <option value="Order">Order</option>
55 <option value="Family">Family</option>
56 <option value="Genus">Genus</option>
57 <option value="Species">Species</option>
58 </param>
59
60
61 <param name="norm_bool" type="boolean" truevalue="true" falsevalue="false" checked="false" label="is the data normalised?"/>
62 <param name="selectedCol" type="data_column" data_ref="meta_table" use_header_names="TRUE" label="Variable to compare"/>
63 <param name="group" type="text" label="Fill in two comparable group separated by comma"/>
64
65 </inputs>
66
67 <outputs>
68 <data format="html" name="htmlfile" label="${tool.name} SymmetricPlot.html"/>
69 </outputs>
70
71 <tests>
72 <test>
73 <param name="input_table" value="count.txt"/>
74 <param name="meta_table" value="metadata.txt"/>
75 <param name="obs_table" value="observation.txt"/>
76 <param name="nTop" value="30"/>
77 <param name="taxonomy_rank" value="Phylum"/>
78 <param name="selectedCol" value="3"/>
79 <param name="group" value="Early,Late"/>
80 <output name="htmlfile" ftype="html" file="SymmetricPlot.html"/></test>
81 </tests>
82 <help>
83 .. class:: infomark
84
85 **TIP:** The input data should be in tabular format.
86
87 .. class:: infomark
88
89 **TIP:** The first column should contain OTU ID.
90
91 .. class:: infomark
92
93 **TIP:** This program takes in two files:1)raw count/normalised table, 2) a metadata file
94
95 .. class:: infomark
96
97 **What it does**
98
99 This program uses an R package called DESeq2_ and ggplot2_ to create a symmetric bar plot.
100
101 .. _DESeq2 : https://bioconductor.org/packages/release/bioc/html/DESeq2.html
102 .. _ggplot2: https://ggplot2.tidyverse.org/
103
104 =======
105 This program uses an R package called DESeq2 and ggplot2 to create a symmetric bar plot.
106
107 -----
108
109 **Syntax**
110
111 This tool creates a symmetric plot based on input table. The input table,if it is a raw count table, will be normalised by DESeq "counts" function with flag "normalised=T".
112
113 - **A normalised dataset** - set to "Yes" only if the input table is a normalised dataset
114 - **Group of choice** - The group of choice will appear in the title of the plot(e.g., Tissue, protein and etc).
115 - **Select a group** - This is a list of group to use in comparison(e.g., Tissue A vs Tissue B). This should be the same as "Group of choice".
116 - **Select only two groups to compare** - select only two groups of interest for comparison.
117
118 -----
119
120 =========
121 Resources
122 =========
123
124 =======
125 **Wrapper Author**
126
127 QFAB Bioinformatics (support@qfab.org)
128
129 </help>
130 <citations>
131 <citation type="doi">10.18129/B9.bioc.DESeq2</citation>
132 <citation type="doi">10.1007/978-3-319-24277-4</citation>
133 </citations>
134 =======
135 </tool>