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comparison melt.xml @ 0:317ed0ee8bf2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
author iuc
date Tue, 22 Aug 2017 07:44:24 -0400
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1 <tool id="melt" name="melt" version="@VERSION@">
2 <description>collapse combinations of variables:values to single lines</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <command detect_errors="exit_code"><![CDATA[
8 cat '$script' &&
9 Rscript '$script'
10 ]]></command>
11 <configfiles>
12 <configfile name="script"><![CDATA[
13 ## Setup R error handling to go to stderr
14 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
16
17 ## Import library
18 library("reshape2")
19
20 input <- read.csv('$input', sep='\t', header=TRUE)
21 minput <- melt(input)
22 write.table(minput, "output.tabular", sep="\t", quote=FALSE, row.names=FALSE)
23
24 ]]></configfile>
25 </configfiles>
26 <inputs>
27 <param name="input" type="data" format="tabular" label="Input should have column headers - these will be the variable IDs that are summarized"/>
28
29 </inputs>
30 <outputs>
31 <data name="output" format="tabular" from_work_dir="output.tabular"/>
32 </outputs>
33 <tests>
34 <test>
35 <param name="input" value="mtcars.txt"/>
36 <output name="output" file="melt_result1.tabular"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40 This tool will apply the melt function of the reshape2 R package.
41
42 The melt function summarizes each unique variable:value combination on a single line. An example can be found here: http://www.statmethods.net/management/reshape.html
43
44 ]]></help>
45 <citations>
46 <citation type="bibtex">
47 @Article{,
48 title = {Reshaping Data with the {reshape} Package},
49 author = {Hadley Wickham},
50 journal = {Journal of Statistical Software},
51 year = {2007},
52 volume = {21},
53 number = {12},
54 pages = {1--20},
55 url = {http://www.jstatsoft.org/v21/i12/},
56 }
57 </citation>
58 </citations>
59 </tool>