annotate cast.xml @ 0:d3b66a3a08ca draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
author iuc
date Tue, 22 Aug 2017 07:44:04 -0400
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d3b66a3a08ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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1 <tool id="cast" name="cast" version="@VERSION@">
d3b66a3a08ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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2 <description>expand combinations of variables:values to columnar format</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <command detect_errors="exit_code"><![CDATA[
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8 cat '$script' &&
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9 Rscript '$script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="script"><![CDATA[
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13 ## Setup R error handling to go to stderr
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14 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
d3b66a3a08ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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16
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17 ## Import library
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18 library("reshape2")
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19
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20 input <- read.csv('$input', sep='\t', header=TRUE)
d3b66a3a08ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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21 cinput <- dcast(input, ... ~ variable)
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22 write.table(cinput, "output.tabular", sep="\t", quote=FALSE, row.names=FALSE)
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23
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24 ]]></configfile>
d3b66a3a08ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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25 </configfiles>
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26 <inputs>
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27 <param name="input" type="data" format="tabular" label="Input should be molten data"/>
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28 </inputs>
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29 <outputs>
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30 <data name="output" format="tabular" from_work_dir="output.tabular"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="melt_result1.tabular"/>
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35 <output name="output" file="cast_result1.tabular"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 This tool will apply the dcast function of the reshape2 R package. The input data should be in a 'long' format or molten by the melt tool. The output will be in a wide format.
d3b66a3a08ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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40 The cast function expands each unique variable:value combination on a single line to columnar format. Documantation on the reshape2 package can be found here: https://cran.r-project.org/web/packages/reshape2/reshape2.pdf
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41 ]]></help>
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42 <citations>
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43 <citation type="bibtex">
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44 @Article{,
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45 title = {Reshaping Data with the {reshape} Package},
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46 author = {Hadley Wickham},
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47 journal = {Journal of Statistical Software},
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48 year = {2007},
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49 volume = {21},
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50 number = {12},
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51 pages = {1--20},
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52 url = {http://www.jstatsoft.org/v21/i12/},
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53 }
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54 </citation>
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55 </citations>
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56 </tool>