Mercurial > repos > iuc > reshape2_melt

annotate 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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317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
iuc
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1 <tool id="melt" name="melt" version="@VERSION@">
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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2 <description>collapse combinations of variables:values to single lines</description>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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3 <macros>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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4 <import>macros.xml</import>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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5 </macros>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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6 <expand macro="requirements"></expand>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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7 <command detect_errors="exit_code"><![CDATA[
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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8 cat '$script' &&
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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9 Rscript '$script'
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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10 ]]></command>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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11 <configfiles>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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12 <configfile name="script"><![CDATA[
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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13 ## Setup R error handling to go to stderr
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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14 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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16
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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17 ## Import library
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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18 library("reshape2")
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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19
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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20 input <- read.csv('$input', sep='\t', header=TRUE)
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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21 minput <- melt(input)
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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22 write.table(minput, "output.tabular", sep="\t", quote=FALSE, row.names=FALSE)
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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23
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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24 ]]></configfile>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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25 </configfiles>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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26 <inputs>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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27 <param name="input" type="data" format="tabular" label="Input should have column headers - these will be the variable IDs that are summarized"/>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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28
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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29 </inputs>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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30 <outputs>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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31 <data name="output" format="tabular" from_work_dir="output.tabular"/>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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32 </outputs>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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33 <tests>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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34 <test>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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35 <param name="input" value="mtcars.txt"/>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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36 <output name="output" file="melt_result1.tabular"/>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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37 </test>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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38 </tests>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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39 <help><![CDATA[
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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40 This tool will apply the melt function of the reshape2 R package.
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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41
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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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
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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43
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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44 ]]></help>
317ed0ee8bf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a
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45 <citations>
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46 <citation type="bibtex">
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47 @Article{,
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48 title = {Reshaping Data with the {reshape} Package},
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49 author = {Hadley Wickham},
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50 journal = {Journal of Statistical Software},
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51 year = {2007},
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52 volume = {21},
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53 number = {12},
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54 pages = {1--20},
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55 url = {http://www.jstatsoft.org/v21/i12/},
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56 }
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57 </citation>
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58 </citations>
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59 </tool>