comparison basicplot.xml @ 0:4b684a42d677 draft

"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/basicplot commit 0dff19dd491024012ea5145323c9f8c527578ca7"
author artbio
date Mon, 06 Jan 2020 12:47:07 -0500
parents
children 42c753143178
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-1:000000000000 0:4b684a42d677
1 <tool id="Basicplot" name="basicplot" version="0.9.1">
2 <description>Basic plot</description>
3 <requirements>
4 <requirement type="package" version="3.5.0">r-base</requirement>
5 </requirements>
6 <command><![CDATA[
7 Rscript '$basicplot' "\${GALAXY_SLOTS:-1}"
8 ]]></command>
9 <configfiles>
10 <configfile name="basicplot">
11 <![CDATA[
12 ## Setup R error handling to go to stderr
13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
14 options(warn=-1)
15 Table = read.delim("${input}", header=TRUE)
16 pdf("${output}")
17 pairs(Table[ ,-1], main="${title}", log="xy", pch = 20)
18 dev.off()
19 ]]>
20 </configfile>
21 </configfiles>
22 <inputs>
23 <param name="input" type="data" format="tabular" label="tabular file"/>
24 <param name="title" type="text" size="25" value="Title" label="Main Title"/>
25 </inputs>
26 <outputs>
27 <data name="output" format="pdf" label="plot" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="input" value="data.tab" ftype="tabular"/>
32 <param name="title" value="Title"/>
33 <output name="output" file="basicplot.pdf" ftype="pdf"/>
34 </test>
35 </tests>
36 <help>
37
38 **What it does**
39
40 Takes a tabular file of numerical data as input and produces pairwise plots of numerical data, in log-log scale.
41 The first column of the data frame is ignored.
42
43 Example of input data:
44
45 <![CDATA[
46
47 gene sample1 sample2 sample3 sample4 sample5 sample6
48
49 tRNA:Ala-AGC-2-3 4407 4506 2267 2423 2736 1153
50
51 tRNA:Asp-GTC-1-10 2111 2931 3302 3499 3809 1682
52
53 tRNA:Asp-GTC-1-11 2099 2936 3349 3556 4124 1629
54
55 tRNA:Glu-TTC-1-6 1095 1376 1189 1162 1120 561
56
57 tRNA:Glu-TTC-1-5 1022 1415 1156 1081 1120 578
58
59 tRNA:Glu-TTC-1-4 1047 1336 1156 1182 1127 602
60
61 tRNA:Glu-CTC-3-4 3613 3414 8161 9021 9776 5248
62
63 tRNA:Glu-CTC-3-5 3741 3292 7893 8845 9833 5074
64
65 tRNA:Glu-CTC-3-6 3619 3379 7663 8737 9513 5021
66
67 tRNA:Glu-CTC-3-8 7249 5809 80760 39479 62652 27404
68
69 tRNA:Glu-CTC-3-9 3770 3367 8007 8969 9976 5100
70
71 ]]>
72
73
74 </help>
75 <citations>
76 <citation type="bibtex">
77 @Manual{,
78 title = {R: A Language and Environment for Statistical Computing},
79 author = {{R Core Team}},
80 organization = {R Foundation for Statistical Computing},
81 address = {Vienna, Austria},
82 year = {2014},
83 url = {http://www.R-project.org/},
84 }
85 </citation>
86 </citations>
87
88 </tool>
89