Mercurial > repos > iuc > ggplot2_boxplot

annotate macros.xml @ 0:204b42a97a97 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 13:01:23 +0000
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0
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
1 <?xml version="1.0"?>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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2 <macros>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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3 <xml name="requirements">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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4 <requirements>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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5 <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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6 <yield />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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7 </requirements>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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8 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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9 <xml name="bio_tools">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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10 <xrefs>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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11 <xref type="bio.tools">ggplot2</xref>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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12 </xrefs>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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13 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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14 <token name="@TOOL_VERSION@">3.5.1</token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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15 <token name="@VERSION_SUFFIX@">1</token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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16
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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17 <token name="@R_INIT@"><![CDATA[
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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18 ## Setup R error handling to go to stderr
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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19 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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20
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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21 ## Unify locale settings
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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22 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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23 ]]></token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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24
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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25 <token name="@TRANSFORM@"><![CDATA[
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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26 #if $adv.transform == "log2"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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27 input["value"] <- log2(input["value"])
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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28 #elif $adv.transform == "log2plus1"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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29 input["value"] <- log2(input["value"]+1)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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30 #elif $adv.transform == "log10"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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31 input["value"] <- log10(input["value"])
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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32 #elif $adv.transform == "log10plus1"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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33 input["value"] <- log10(input["value"]+1)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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34 #end if
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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35 ]]></token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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36
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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37 <token name="@XY_SCALING@"><![CDATA[
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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38 #Choose between automatically scaled x and y axis or user defined
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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39 #if $adv.scaling.plot_scaling == "Automatic"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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40 gg_scalex = NULL
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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41 gg_scaley = NULL
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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42 #else
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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43 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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44 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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45 cat("\n xaxismin: ", $adv.scaling.xaxismin)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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46 cat("\n xaxismax: ", $adv.scaling.xaxismax)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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47 cat("\n yaxismin: ", $adv.scaling.yaxismin)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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48 cat("\n yaxismax: ", $adv.scaling.yaxismax)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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49 #end if
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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50 ]]></token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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51
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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52 <token name="@THEME@"><![CDATA[
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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53 ## Choose theme for plot
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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54 #if $adv.theme == "bw"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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55 gg_theme = theme_bw()
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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56 #else
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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57 gg_theme = NULL
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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58 #end if
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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59 ]]></token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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60
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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61 <token name="@LEGEND@"><![CDATA[
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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62 ## Show/hide legend
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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63 #if $adv.legend == "yes"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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64 gg_legend = theme(legend.position="right")
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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65 #else
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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66 gg_legend = theme(legend.position="none")
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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67 cat("\n no legend")
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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68 #end if
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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69 ]]></token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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70 <token name="@SAVE_OUTPUT@"><![CDATA[
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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71 ## output options need to be in out section
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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72 gg_width <- as.double('$out.width_output_dim')
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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73 gg_height <- as.double('$out.height_output_dim')
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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74 gg_unit <- '$out.unit_output_dim'
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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75 gg_dpi <- as.double('$out.dpi_output_dim')
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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76 gg_add_device <- '$out.additional_output_format'
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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77 output1 <- '$output1'
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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78 output2 <- '$output2'
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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79
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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80 ## ggsave to png
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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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")
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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82 if(gg_add_device != "none"){
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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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)
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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84 }
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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85 ]]></token>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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86 <xml name="read_complex_input">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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87 <param name="input1" type="data" format="tabular" label="Select table"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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88 <conditional name="inputdata">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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89 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
90 <option value="with_header" selected="true">Dataset with header</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
91 <option value="with_rownames">Dataset with row names</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
92 <option value="with_header_rownames">Dataset with header and row names</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
93 <option value="no_header_rownames">Dataset without header or row names</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
94 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
95 <when value="with_header">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
96 <param name="header" type="hidden" value="TRUE"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
97 <param name="row_names_index" type="hidden" value="0"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
99 <option value="TRUE" selected="true">horizontal</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
100 <option value="FALSE">vertial</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
101 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
102 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
103 <when value="with_rownames">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
104 <param name="header" type="hidden" value="FALSE"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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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"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
107 <option value="TRUE">horizontal</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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108 <option value="FALSE" selected="true">vertial</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
109 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
110 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
111 <when value="with_header_rownames">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
112 <param name="header" type="hidden" value="TRUE"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
115 <option value="TRUE" selected="true">horizontal</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
116 <option value="FALSE">vertial</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
117 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
118 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
119 <when value="no_header_rownames">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
120 <param name="header" type="hidden" value="FALSE"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
121 <param name="row_names_index" type="hidden" value="0"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
122 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
123 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
124 </conditional>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
125 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
126 <xml name="transform">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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127 <param name="transform" type="select" label="Data transformation">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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128 <option value="none">Plot the data as it is</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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129 <option value="log2">Log2(value) transform my data</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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130 <option value="log2plus1">Log2(value+1) transform my data</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
131 <option value="log10">Log10(value) transform my data</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
132 <option value="log10plus1">Log10(value+1) transform my data</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
133 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
134 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
135 <xml name="xy_scaling">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
136 <conditional name="scaling">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
137 <param name="plot_scaling" type="select" label="Axis scaling">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
138 <option value="Automatic" selected="true">Automatic axis scaling</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
139 <option value="Defined">User-defined axis scales</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
140 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
141 <when value="Automatic"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
142 <when value="Defined">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
143 <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
144 <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
145 <param name="yaxismin" type="float" value="0" label="minimal range of y-axis" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
146 <param name="yaxismax" type="float" value="3" label="maximal range of y-axis" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
147 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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148 </conditional>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
149 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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150 <xml name="title">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
151 <param name="title" type="text" value="" label="Plot title">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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152 <!--<sanitizer sanitize="false"/> -->
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
153 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
154 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
155 <xml name="xy_lab">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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156 <param name="xlab" type="text" value="Title of x-axis" label="Label for x axis">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
157 <sanitizer sanitize="false"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
158 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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159 <param name="ylab" type="text" value="Title of y-axis" label="Label for y axis">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
160 <sanitizer sanitize="false"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
161 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
162 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
163 <xml name="legend">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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164 <param name="legend" type="select" label="Legend options">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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165 <option value="yes">Include legend on plot</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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166 <option value="no">Hide legend</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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167 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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168 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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169 <xml name="theme">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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170 <param name="theme" type="select" label="Backgound theme for plot">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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171 <option value="bw">Black and white</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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172 <option value="Default">Default (grey)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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173 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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174 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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175 <xml name="dimensions">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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176 <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="Default: inches.">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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177 <option value="in" selected="true">Inches (in)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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178 <option value="cm">Centimeters (cm)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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179 <option value="mm">Millimeters (mm)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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180 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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181 <param name="width_output_dim" type="float" value="7" label="width of output"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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182 <param name="height_output_dim" type="float" value="7" label="height of output"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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183 <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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184 <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format.">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents:
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185 <option value="none" selected="true">Only PNG</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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186 <option value="pdf">PDF</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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187 <option value="svg">SVG</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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188 <option value="eps">EPS</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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189 <option value="ps">PS</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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190 <option value="tex">TEX (pictex)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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191 <option value="jpeg">JPEG</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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192 <option value="tiff">TIFF</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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193 <option value="bmp">BMP</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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194 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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195 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
196 <xml name="citations">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
197 <citations>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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198 <citation type="bibtex">@book{wickham2009ggplot2,
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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199 author = {Hadley Wickham},
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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200 title = {ggplot2: Elegant Graphics for Data Analysis},
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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201 publisher = {Springer-Verlag New York},
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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202 year = {2009},
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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203 isbn = {978-0-387-98140-6},
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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204 url = {https://ggplot2.tidyverse.org/},
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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205 }
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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206 </citation>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
207 <yield />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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208 </citations>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
209 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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210 <xml name="axis_customization" token_label="Axis title options">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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211 <param name="axis_customization" type="select" label="@LABEL@">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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212 <option value="default" selected="true">Default</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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213 <option value="defined">User defined label options</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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214 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
215 <when value="default"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
216 <when value="defined">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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217 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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218 <param name="color" type="select" label="Color of axis label">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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219 <option value="black">Black (default)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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220 <option value="red">Red</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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221 <option value="white">White</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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222 <option value="blue">Blue</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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223 <option value="orange">Orange</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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224 <option value="yellow">Yellow</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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225 <option value="green">Green</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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226 <option value="purple">Purple</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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227 <option value="magenta">Magenta</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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228 <option value="cyan">Cyan</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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229 <option value="grey">Grey</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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230 <option value="gold">Gold</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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231 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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232 <param name="face" type="select" label="Font effect of axis label">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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233 <option value="plain">Normal (default)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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234 <option value="bold">Bold</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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235 <option value="italic">Italic</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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236 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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237 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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238 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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239 <xml name="colors">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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240 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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241 <option value="Default">Default color scheme</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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242 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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243 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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244 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
245 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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246 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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247 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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248 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
249 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
250 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
251 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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252 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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253 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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254 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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255 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
256 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
257 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
258 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
259 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
260 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
261 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
262 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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263 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
264 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
265 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
266 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
267 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
268 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
269 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
270 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
271 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
272 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
273 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
274 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
275 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
276 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
277 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
278 <xml name="additional_output">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
279 <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
280 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
281 <change_format>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
282 <when input="out.additional_output_format" value="svg" format="svg" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
283 <when input="out.additional_output_format" value="eps" format="eps" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
284 <when input="out.additional_output_format" value="ps" format="ps" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
285 <when input="out.additional_output_format" value="tex" format="txt" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
286 <when input="out.additional_output_format" value="jpeg" format="jpg" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
287 <when input="out.additional_output_format" value="tiff" format="tiff" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
288 <when input="out.additional_output_format" value="bmp" format="bmp" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
289 </change_format>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
290 <filter>out['additional_output_format'] != "none"</filter>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
291 </data>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
292 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
293 <xml name="points_options">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
294 <conditional name="points">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
295 <param name="pointoptions" type="select" label="Data point options">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
296 <option value="default" selected="true">Default</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
297 <option value="defined">User defined point options</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
298 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
299 <when value="default">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
300 <!--Do nothing here -->
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
301 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
302 <when value="defined">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
303 <param name="size" type="float" value="1" label="relative size of points" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
304 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
305 <param name="pointcolor" type="select" label="Color of data points" >
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
306 <option value="black">Black (default)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
307 <option value="red">Red</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
308 <option value="white">White</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
309 <option value="blue">Blue</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
310 <option value="orange">Orange</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
311 <option value="yellow">Yellow</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
312 <option value="green">Green</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
313 <option value="purple">Purple</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
314 <option value="magenta">Magenta</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
315 <option value="cyan">Cyan</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
316 <option value="grey">Grey</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
317 <option value="gold">Gold</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
318 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
319 <param name="shape" type="select" label="Shape of data points" >
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
320 <option value="0">square</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
321 <option value="1">circle</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
322 <option value="2">triangle point up</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
323 <option value="3">plus</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
324 <option value="4">cross</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
325 <option value="5">diamond</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
326 <option value="6">triangle point down</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
327 <option value="7">square cross</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
328 <option value="8">star</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
329 <option value="9">diamond plus</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
330 <option value="10">circle plus</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
331 <option value="11">triangles up and down</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
332 <option value="12">square plus</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
333 <option value="13">circle cross</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
334 <option value="14">square and triangle down</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
335 <option value="15">filled square</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
336 <option value="16">filled circle</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
337 <option value="17">filled triangle point-up</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
338 <option value="18">filled diamond</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
339 <option value="19">solid circle</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
340 <option value="20">bullet (smaller circle)</option>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
341 </param>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
342 </when>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
343 </conditional>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
344 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
345 <xml name="data_input">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
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"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
347 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
348
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
349 <xml name="axes_labels">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
350 <param name="xlab" type="text" label="Label for the x axis" optional="true"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
351 <param name="ylab" type="text" label="Label for the y axis" optional="true"/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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352 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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353
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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354 <xml name="export_data">
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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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"
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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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."/>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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357 </xml>
204b42a97a97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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358 </macros>