Mercurial > repos > qfabrepo > metadegalaxy_symmetric_plot
comparison symmetric_plot.xml @ 0:0cac08094b86 draft
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/symmetric_plot commit a68579d7bdde7420b8f04346d3b6e361588acf50"
author | qfabrepo |
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date | Mon, 14 Sep 2020 06:04:44 +0000 |
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children | 680917d9d415 |
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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> |