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comparison symmetric_plot.xml @ 1:680917d9d415 draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/symmetric_plot commit 92c83b79fb5a8c0db6b049f10c4ffd8eb8b10748"
author qfabrepo
date Mon, 14 Sep 2020 06:20:40 +0000
parents 0cac08094b86
children
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0:0cac08094b86 1:680917d9d415
5 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement> 5 <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
6 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> 6 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement> 7 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="0.6.3">r-tidyr</requirement> 8 <requirement type="package" version="0.6.3">r-tidyr</requirement>
9 <requirement type="package" version="9.18">ghostscript</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> 10 </requirements>
20 <version_command><![CDATA[ 11 <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: ") 12 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> 13 ]]></version_command>
23 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
78 <param name="selectedCol" value="3"/> 69 <param name="selectedCol" value="3"/>
79 <param name="group" value="Early,Late"/> 70 <param name="group" value="Early,Late"/>
80 <output name="htmlfile" ftype="html" file="SymmetricPlot.html"/></test> 71 <output name="htmlfile" ftype="html" file="SymmetricPlot.html"/></test>
81 </tests> 72 </tests>
82 <help> 73 <help>
74
83 .. class:: infomark 75 .. class:: infomark
84 76
85 **TIP:** The input data should be in tabular format. 77 **TIP:** The input data should be in tabular format.
86 78
87 .. class:: infomark 79 .. class:: infomark
99 This program uses an R package called DESeq2_ and ggplot2_ to create a symmetric bar plot. 91 This program uses an R package called DESeq2_ and ggplot2_ to create a symmetric bar plot.
100 92
101 .. _DESeq2 : https://bioconductor.org/packages/release/bioc/html/DESeq2.html 93 .. _DESeq2 : https://bioconductor.org/packages/release/bioc/html/DESeq2.html
102 .. _ggplot2: https://ggplot2.tidyverse.org/ 94 .. _ggplot2: https://ggplot2.tidyverse.org/
103 95
104 =======
105 This program uses an R package called DESeq2 and ggplot2 to create a symmetric bar plot.
106
107 ----- 96 -----
108 97
109 **Syntax** 98 **Syntax**
110 99
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". 100 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".
119 108
120 ========= 109 =========
121 Resources 110 Resources
122 ========= 111 =========
123 112
124 =======
125 **Wrapper Author** 113 **Wrapper Author**
126 114
127 QFAB Bioinformatics (support@qfab.org) 115 QFAB Bioinformatics (support@qfab.org)
128 116
129 </help> 117 </help>
130 <citations> 118 <citations>
131 <citation type="doi">10.18129/B9.bioc.DESeq2</citation> 119 <citation type="doi">10.18129/B9.bioc.DESeq2</citation>
132 <citation type="doi">10.1007/978-3-319-24277-4</citation> 120 <citation type="doi">10.1007/978-3-319-24277-4</citation>
133 </citations> 121 </citations>
134 =======
135 </tool> 122 </tool>