Mercurial > repos > iuc > ggplot2_heatmap

annotate macros.xml @ 10:15cebddc6dba draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
author iuc
date Thu, 15 May 2025 13:02:40 +0000
parents 1a72f938213e
children
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f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
1 <?xml version="1.0"?>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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2 <macros>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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3 <xml name="requirements">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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4 <requirements>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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5 <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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6 <yield />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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7 </requirements>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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8 </xml>
4
391a4cc45fea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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9 <xml name="bio_tools">
391a4cc45fea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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10 <xrefs>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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11 <xref type="bio.tools">ggplot2</xref>
4
391a4cc45fea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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12 </xrefs>
391a4cc45fea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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13 </xml>
10
15cebddc6dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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14 <token name="@TOOL_VERSION@">3.5.1</token>
9
1a72f938213e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
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15 <token name="@VERSION_SUFFIX@">1</token>
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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17 <token name="@R_INIT@"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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18 ## Setup R error handling to go to stderr
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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19 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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21 ## Unify locale settings
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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23 ]]></token>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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24
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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25 <token name="@TRANSFORM@"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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26 #if $adv.transform == "log2"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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27 input["value"] <- log2(input["value"])
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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28 #elif $adv.transform == "log2plus1"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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29 input["value"] <- log2(input["value"]+1)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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30 #elif $adv.transform == "log10"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 input["value"] <- log10(input["value"])
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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32 #elif $adv.transform == "log10plus1"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33 input["value"] <- log10(input["value"]+1)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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34 #end if
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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35 ]]></token>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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36
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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37 <token name="@XY_SCALING@"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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38 #Choose between automatically scaled x and y axis or user defined
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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39 #if $adv.scaling.plot_scaling == "Automatic"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 gg_scalex = NULL
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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41 gg_scaley = NULL
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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42 #else
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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43 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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44 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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45 cat("\n xaxismin: ", $adv.scaling.xaxismin)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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46 cat("\n xaxismax: ", $adv.scaling.xaxismax)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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47 cat("\n yaxismin: ", $adv.scaling.yaxismin)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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48 cat("\n yaxismax: ", $adv.scaling.yaxismax)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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49 #end if
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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50 ]]></token>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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51
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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52 <token name="@THEME@"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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53 ## Choose theme for plot
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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54 #if $adv.theme == "bw"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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55 gg_theme = theme_bw()
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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56 #else
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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57 gg_theme = NULL
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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58 #end if
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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59 ]]></token>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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60
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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61 <token name="@LEGEND@"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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62 ## Show/hide legend
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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63 #if $adv.legend == "yes"
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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64 gg_legend = theme(legend.position="right")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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65 #else
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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66 gg_legend = theme(legend.position="none")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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67 cat("\n no legend")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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68 #end if
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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69 ]]></token>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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70 <token name="@SAVE_OUTPUT@"><![CDATA[
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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71 ## output options need to be in out section
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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72 gg_width <- as.double('$out.width_output_dim')
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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73 gg_height <- as.double('$out.height_output_dim')
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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74 gg_unit <- '$out.unit_output_dim'
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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75 gg_dpi <- as.double('$out.dpi_output_dim')
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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76 gg_add_device <- '$out.additional_output_format'
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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77 output1 <- '$output1'
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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78 output2 <- '$output2'
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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79
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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80 ## ggsave to png
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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81 ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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82 if(gg_add_device != "none"){
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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83 ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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84 }
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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85 ]]></token>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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86 <xml name="read_complex_input">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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87 <param name="input1" type="data" format="tabular" label="Select table"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
88 <conditional name="inputdata">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
89 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
90 <option value="with_header" selected="true">Dataset with header</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
91 <option value="with_rownames">Dataset with row names</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
92 <option value="with_header_rownames">Dataset with header and row names</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
93 <option value="no_header_rownames">Dataset without header or row names</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
94 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
95 <when value="with_header">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
96 <param name="header" type="hidden" value="TRUE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
97 <param name="row_names_index" type="hidden" value="0"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
98 <param name="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
99 <option value="TRUE" selected="true">horizontal</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
100 <option value="FALSE">vertial</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
101 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
102 </when>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
103 <when value="with_rownames">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
104 <param name="header" type="hidden" value="FALSE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
105 <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
106 <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
107 <option value="TRUE">horizontal</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
108 <option value="FALSE" selected="true">vertial</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
109 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
110 </when>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
111 <when value="with_header_rownames">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
112 <param name="header" type="hidden" value="TRUE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
113 <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
114 <param name="sample_name_orientation" type="select" label="Sample names orientation" display="radio" multiple="false" help="deside whether header names or row names are interpreted as sample names">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
115 <option value="TRUE" selected="true">horizontal</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
116 <option value="FALSE">vertial</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
117 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
118 </when>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
119 <when value="no_header_rownames">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
120 <param name="header" type="hidden" value="FALSE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
121 <param name="row_names_index" type="hidden" value="0"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
122 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
123 </when>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
124 </conditional>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
125 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
126 <xml name="transform">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
127 <param name="transform" type="select" label="Data transformation">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
128 <option value="none">Plot the data as it is</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
129 <option value="log2">Log2(value) transform my data</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
130 <option value="log2plus1">Log2(value+1) transform my data</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
131 <option value="log10">Log10(value) transform my data</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
132 <option value="log10plus1">Log10(value+1) transform my data</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
133 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
134 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
135 <xml name="xy_scaling">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
136 <conditional name="scaling">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
137 <param name="plot_scaling" type="select" label="Axis scaling">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
138 <option value="Automatic" selected="true">Automatic axis scaling</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
139 <option value="Defined">User-defined axis scales</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
140 </param>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
141 <when value="Automatic"/>
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
142 <when value="Defined">
2
de002ba2b849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
iuc
parents: 0
diff changeset
143 <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
de002ba2b849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
iuc
parents: 0
diff changeset
144 <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
de002ba2b849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
iuc
parents: 0
diff changeset
145 <param name="yaxismin" type="float" value="0" label="minimal range of y-axis" />
de002ba2b849 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
iuc
parents: 0
diff changeset
146 <param name="yaxismax" type="float" value="3" label="maximal range of y-axis" />
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
147 </when>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
148 </conditional>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
149 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
150 <xml name="title">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
151 <param name="title" type="text" value="" label="Plot title">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
152 <!--<sanitizer sanitize="false"/> -->
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
153 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
154 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
155 <xml name="xy_lab">
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
156 <param name="xlab" type="text" value="Title of x-axis" label="Label for x axis">
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
157 <sanitizer sanitize="false"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
158 </param>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
159 <param name="ylab" type="text" value="Title of y-axis" label="Label for y axis">
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
160 <sanitizer sanitize="false"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
161 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
162 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
163 <xml name="legend">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
164 <param name="legend" type="select" label="Legend options">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
165 <option value="yes">Include legend on plot</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
166 <option value="no">Hide legend</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
167 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
168 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
169 <xml name="theme">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
170 <param name="theme" type="select" label="Backgound theme for plot">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
171 <option value="bw">Black and white</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
172 <option value="Default">Default (grey)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
173 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
174 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
175 <xml name="dimensions">
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
176 <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="Default: inches.">
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
177 <option value="in" selected="true">Inches (in)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
178 <option value="cm">Centimeters (cm)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
179 <option value="mm">Millimeters (mm)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
180 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
181 <param name="width_output_dim" type="float" value="7" label="width of output"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
182 <param name="height_output_dim" type="float" value="7" label="height of output"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
183 <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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parents: 4
diff changeset
184 <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format.">
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
185 <option value="none" selected="true">Only PNG</option>
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
186 <option value="pdf">PDF</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
187 <option value="svg">SVG</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
188 <option value="eps">EPS</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
189 <option value="ps">PS</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
190 <option value="tex">TEX (pictex)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
191 <option value="jpeg">JPEG</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
192 <option value="tiff">TIFF</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
193 <option value="bmp">BMP</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
194 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
195 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
196 <xml name="citations">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
197 <citations>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
198 <citation type="bibtex">@book{wickham2009ggplot2,
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
199 author = {Hadley Wickham},
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
200 title = {ggplot2: Elegant Graphics for Data Analysis},
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
201 publisher = {Springer-Verlag New York},
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
202 year = {2009},
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
203 isbn = {978-0-387-98140-6},
3
a4d83ba2a1bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 8e0f13edc2c06772dac0c1258e362045e68028b8"
iuc
parents: 2
diff changeset
204 url = {https://ggplot2.tidyverse.org/},
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
205 }
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
206 </citation>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
207 <yield />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
208 </citations>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
209 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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210 <xml name="axis_customization" token_label="Axis title options">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
211 <param name="axis_customization" type="select" label="@LABEL@">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
212 <option value="default" selected="true">Default</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
213 <option value="defined">User defined label options</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
214 </param>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
215 <when value="default"/>
0
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
216 <when value="defined">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
217 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
218 <param name="color" type="select" label="Color of axis label">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
219 <option value="black">Black (default)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
220 <option value="red">Red</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
221 <option value="white">White</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
222 <option value="blue">Blue</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
223 <option value="orange">Orange</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
224 <option value="yellow">Yellow</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
225 <option value="green">Green</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
226 <option value="purple">Purple</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
227 <option value="magenta">Magenta</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
228 <option value="cyan">Cyan</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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229 <option value="grey">Grey</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
230 <option value="gold">Gold</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
231 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
232 <param name="face" type="select" label="Font effect of axis label">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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233 <option value="plain">Normal (default)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
234 <option value="bold">Bold</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
235 <option value="italic">Italic</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
236 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
237 </when>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
238 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
239 <xml name="colors">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
240 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
241 <option value="Default">Default color scheme</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
242 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
243 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
244 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
245 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
246 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
247 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
248 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
249 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
250 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
251 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
252 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
253 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
254 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
255 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
256 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
257 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
258 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
259 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
260 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
261 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
262 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
263 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
264 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
265 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
266 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
267 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
268 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
269 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
270 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
271 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
272 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
273 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
274 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
275 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
276 </param>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
277 </xml>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
278 <xml name="additional_output">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
279 <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
280 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
281 <change_format>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
282 <when input="out.additional_output_format" value="svg" format="svg" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
283 <when input="out.additional_output_format" value="eps" format="eps" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
284 <when input="out.additional_output_format" value="ps" format="ps" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
285 <when input="out.additional_output_format" value="tex" format="txt" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
286 <when input="out.additional_output_format" value="jpeg" format="jpg" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
287 <when input="out.additional_output_format" value="tiff" format="tiff" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
288 <when input="out.additional_output_format" value="bmp" format="bmp" />
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
289 </change_format>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
290 <filter>out['additional_output_format'] != "none"</filter>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
291 </data>
f44dc95928aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
292 </xml>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
293 <xml name="points_options">
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
294 <conditional name="points">
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
295 <param name="pointoptions" type="select" label="Data point options">
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
296 <option value="default" selected="true">Default</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
297 <option value="defined">User defined point options</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
298 </param>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
299 <when value="default">
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
300 <!--Do nothing here -->
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
301 </when>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
302 <when value="defined">
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
303 <param name="size" type="float" value="1" label="relative size of points" />
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
304 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
305 <param name="pointcolor" type="select" label="Color of data points" >
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
306 <option value="black">Black (default)</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
307 <option value="red">Red</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
308 <option value="white">White</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
309 <option value="blue">Blue</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
310 <option value="orange">Orange</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
311 <option value="yellow">Yellow</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
312 <option value="green">Green</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
313 <option value="purple">Purple</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
314 <option value="magenta">Magenta</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
315 <option value="cyan">Cyan</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
316 <option value="grey">Grey</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
317 <option value="gold">Gold</option>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
318 </param>
6
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
319 <param name="shape" type="select" label="Shape of data points" >
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
320 <option value="0">square</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
321 <option value="1">circle</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
322 <option value="2">triangle point up</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
323 <option value="3">plus</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
324 <option value="4">cross</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
325 <option value="5">diamond</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
326 <option value="6">triangle point down</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
327 <option value="7">square cross</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
328 <option value="8">star</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
329 <option value="9">diamond plus</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
330 <option value="10">circle plus</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
331 <option value="11">triangles up and down</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
332 <option value="12">square plus</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
333 <option value="13">circle cross</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
334 <option value="14">square and triangle down</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
335 <option value="15">filled square</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
336 <option value="16">filled circle</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
337 <option value="17">filled triangle point-up</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
338 <option value="18">filled diamond</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
339 <option value="19">solid circle</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
340 <option value="20">bullet (smaller circle)</option>
3d059e9c2fba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 5
diff changeset
341 </param>
5
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
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342 </when>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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343 </conditional>
d3a9e32672ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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344 </xml>
10
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345 <xml name="data_input">
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346 <param name="input_data" type="data" format="csv,tsv,txt,tabular,parquet" label="Input table" help= "Input file in a tabular/tsv/csv/parquet format"/>
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347 </xml>
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348
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349 <xml name="axes_labels">
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350 <param name="xlab" type="text" label="Label for the x axis" optional="true"/>
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351 <param name="ylab" type="text" label="Label for the y axis" optional="true"/>
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352 </xml>
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353
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354 <xml name="export_data">
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355 <param name="export_R_script" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export the R script to reproduce the analysis"
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356 help="Check this box to export the script executed in the Galaxy tool as an R file to be able to reproduce the same processing offline. Not that in this case, the file paths need to be altered and all the dependencies have to be managed manually."/>
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357 </xml>
0
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358 </macros>