Mercurial > repos > iuc > ggplot2_barplot

annotate macros.xml @ 0:f098df64f6ad 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 13:00:48 +0000
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0
f098df64f6ad 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"?>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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2 <macros>
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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4 <requirements>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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6 <yield />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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7 </requirements>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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8 </xml>
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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10 <xrefs>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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11 <xref type="bio.tools">ggplot2</xref>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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12 </xrefs>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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13 </xml>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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16
f098df64f6ad 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[
f098df64f6ad 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
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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19 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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20
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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21 ## Unify locale settings
f098df64f6ad 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")
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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23 ]]></token>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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24
f098df64f6ad 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[
f098df64f6ad 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"
f098df64f6ad 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"])
f098df64f6ad 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"
f098df64f6ad 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)
f098df64f6ad 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"
f098df64f6ad 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"])
f098df64f6ad 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"
f098df64f6ad 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)
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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34 #end if
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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35 ]]></token>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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36
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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37 <token name="@XY_SCALING@"><![CDATA[
f098df64f6ad 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
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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39 #if $adv.scaling.plot_scaling == "Automatic"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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40 gg_scalex = NULL
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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41 gg_scaley = NULL
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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42 #else
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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43 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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44 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
f098df64f6ad 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)
f098df64f6ad 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)
f098df64f6ad 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)
f098df64f6ad 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)
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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49 #end if
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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50 ]]></token>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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51
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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52 <token name="@THEME@"><![CDATA[
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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53 ## Choose theme for plot
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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54 #if $adv.theme == "bw"
f098df64f6ad 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()
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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56 #else
f098df64f6ad 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
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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58 #end if
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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59 ]]></token>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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60
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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61 <token name="@LEGEND@"><![CDATA[
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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62 ## Show/hide legend
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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63 #if $adv.legend == "yes"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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64 gg_legend = theme(legend.position="right")
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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65 #else
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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66 gg_legend = theme(legend.position="none")
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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67 cat("\n no legend")
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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68 #end if
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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69 ]]></token>
f098df64f6ad 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[
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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71 ## output options need to be in out section
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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72 gg_width <- as.double('$out.width_output_dim')
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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73 gg_height <- as.double('$out.height_output_dim')
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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74 gg_unit <- '$out.unit_output_dim'
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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75 gg_dpi <- as.double('$out.dpi_output_dim')
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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76 gg_add_device <- '$out.additional_output_format'
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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77 output1 <- '$output1'
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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78 output2 <- '$output2'
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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79
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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80 ## ggsave to png
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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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")
f098df64f6ad 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"){
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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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)
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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84 }
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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85 ]]></token>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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86 <xml name="read_complex_input">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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87 <param name="input1" type="data" format="tabular" label="Select table"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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88 <conditional name="inputdata">
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents:
diff changeset
90 <option value="with_header" selected="true">Dataset with header</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
94 </param>
f098df64f6ad 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">
f098df64f6ad 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"/>
f098df64f6ad 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"/>
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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100 <option value="FALSE">vertial</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
101 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
102 </when>
f098df64f6ad 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">
f098df64f6ad 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"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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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"/>
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
109 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
110 </when>
f098df64f6ad 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">
f098df64f6ad 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"/>
f098df64f6ad 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"/>
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
117 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
118 </when>
f098df64f6ad 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">
f098df64f6ad 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"/>
f098df64f6ad 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"/>
f098df64f6ad 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"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
123 </when>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
124 </conditional>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
125 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
126 <xml name="transform">
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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129 <option value="log2">Log2(value) transform my data</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
133 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
134 </xml>
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
136 <conditional name="scaling">
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
140 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
141 <when value="Automatic"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
142 <when value="Defined">
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
147 </when>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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148 </conditional>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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149 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
150 <xml name="title">
f098df64f6ad 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">
f098df64f6ad 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"/> -->
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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153 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
154 </xml>
f098df64f6ad 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">
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
157 <sanitizer sanitize="false"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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diff changeset
158 </param>
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
160 <sanitizer sanitize="false"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
161 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
162 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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163 <xml name="legend">
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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167 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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168 </xml>
f098df64f6ad 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">
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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172 <option value="Default">Default (grey)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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173 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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174 </xml>
f098df64f6ad 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">
f098df64f6ad 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.">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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179 <option value="mm">Millimeters (mm)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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180 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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181 <param name="width_output_dim" type="float" value="7" label="width of output"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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182 <param name="height_output_dim" type="float" value="7" label="height of output"/>
f098df64f6ad 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."/>
f098df64f6ad 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.">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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185 <option value="none" selected="true">Only PNG</option>
f098df64f6ad 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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186 <option value="pdf">PDF</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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187 <option value="svg">SVG</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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188 <option value="eps">EPS</option>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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190 <option value="tex">TEX (pictex)</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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194 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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195 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
196 <xml name="citations">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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197 <citations>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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198 <citation type="bibtex">@book{wickham2009ggplot2,
f098df64f6ad 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},
f098df64f6ad 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},
f098df64f6ad 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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201 publisher = {Springer-Verlag New York},
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents:
diff changeset
202 year = {2009},
f098df64f6ad 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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203 isbn = {978-0-387-98140-6},
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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204 url = {https://ggplot2.tidyverse.org/},
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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205 }
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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206 </citation>
f098df64f6ad 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 />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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208 </citations>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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210 <xml name="axis_customization" token_label="Axis title options">
f098df64f6ad 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@">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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214 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
215 <when value="default"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
216 <when value="defined">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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217 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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218 <param name="color" type="select" label="Color of axis label">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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222 <option value="blue">Blue</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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227 <option value="magenta">Magenta</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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228 <option value="cyan">Cyan</option>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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230 <option value="gold">Gold</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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231 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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232 <param name="face" type="select" label="Font effect of axis label">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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233 <option value="plain">Normal (default)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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234 <option value="bold">Bold</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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235 <option value="italic">Italic</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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236 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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237 </when>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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238 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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239 <xml name="colors">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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240 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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241 <option value="Default">Default color scheme</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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242 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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245 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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246 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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248 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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249 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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250 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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256 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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257 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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259 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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260 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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261 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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262 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
276 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
277 </xml>
f098df64f6ad 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">
f098df64f6ad 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 ${on_string}: png"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
280 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
281 <change_format>
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad 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" />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
289 </change_format>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
291 </data>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
292 </xml>
f098df64f6ad 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">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
294 <conditional name="points">
f098df64f6ad 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">
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
298 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
299 <when value="default">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
300 <!--Do nothing here -->
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
301 </when>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
302 <when value="defined">
f098df64f6ad 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" />
f098df64f6ad 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)" />
f098df64f6ad 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" >
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
318 </param>
f098df64f6ad 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" >
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad 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>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
341 </param>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
342 </when>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
343 </conditional>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
344 </xml>
f098df64f6ad 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">
f098df64f6ad 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"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
347 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
diff changeset
348
f098df64f6ad 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">
f098df64f6ad 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"/>
f098df64f6ad 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"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents:
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352 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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353
f098df64f6ad 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">
f098df64f6ad 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"
f098df64f6ad 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."/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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357 </xml>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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358 </macros>