annotate macros.xml @ 8:8b8a26a5fdf2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
author iuc
date Thu, 15 May 2025 13:01:32 +0000
parents 48fc850095ba
children
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d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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1 <?xml version="1.0"?>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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2 <macros>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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3 <xml name="requirements">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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4 <requirements>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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5 <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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6 <yield />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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7 </requirements>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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8 </xml>
4
5acfed72fb36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9 <xml name="bio_tools">
5acfed72fb36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <xrefs>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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11 <xref type="bio.tools">ggplot2</xref>
4
5acfed72fb36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 </xrefs>
5acfed72fb36 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 </xml>
8
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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14 <token name="@TOOL_VERSION@">3.5.1</token>
7
48fc850095ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
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15 <token name="@VERSION_SUFFIX@">1</token>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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16
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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17 <token name="@R_INIT@"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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18 ## Setup R error handling to go to stderr
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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19 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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20
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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21 ## Unify locale settings
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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23 ]]></token>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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24
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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25 <token name="@TRANSFORM@"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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26 #if $adv.transform == "log2"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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27 input["value"] <- log2(input["value"])
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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28 #elif $adv.transform == "log2plus1"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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29 input["value"] <- log2(input["value"]+1)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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30 #elif $adv.transform == "log10"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 input["value"] <- log10(input["value"])
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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32 #elif $adv.transform == "log10plus1"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33 input["value"] <- log10(input["value"]+1)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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34 #end if
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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35 ]]></token>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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36
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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37 <token name="@XY_SCALING@"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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38 #Choose between automatically scaled x and y axis or user defined
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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39 #if $adv.scaling.plot_scaling == "Automatic"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 gg_scalex = NULL
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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41 gg_scaley = NULL
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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42 #else
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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43 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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44 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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45 cat("\n xaxismin: ", $adv.scaling.xaxismin)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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46 cat("\n xaxismax: ", $adv.scaling.xaxismax)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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47 cat("\n yaxismin: ", $adv.scaling.yaxismin)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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48 cat("\n yaxismax: ", $adv.scaling.yaxismax)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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49 #end if
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50 ]]></token>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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51
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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52 <token name="@THEME@"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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53 ## Choose theme for plot
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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54 #if $adv.theme == "bw"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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55 gg_theme = theme_bw()
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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56 #else
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57 gg_theme = NULL
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58 #end if
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59 ]]></token>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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60
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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61 <token name="@LEGEND@"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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62 ## Show/hide legend
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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63 #if $adv.legend == "yes"
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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64 gg_legend = theme(legend.position="right")
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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65 #else
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66 gg_legend = theme(legend.position="none")
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67 cat("\n no legend")
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68 #end if
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69 ]]></token>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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70 <token name="@SAVE_OUTPUT@"><![CDATA[
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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71 ## output options need to be in out section
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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72 gg_width <- as.double('$out.width_output_dim')
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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73 gg_height <- as.double('$out.height_output_dim')
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74 gg_unit <- '$out.unit_output_dim'
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75 gg_dpi <- as.double('$out.dpi_output_dim')
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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76 gg_add_device <- '$out.additional_output_format'
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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77 output1 <- '$output1'
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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78 output2 <- '$output2'
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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79
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80 ## ggsave to png
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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81 ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
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82 if(gg_add_device != "none"){
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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83 ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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84 }
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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85 ]]></token>
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86 <xml name="read_complex_input">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
87 <param name="input1" type="data" format="tabular" label="Select table"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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88 <conditional name="inputdata">
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89 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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90 <option value="with_header" selected="true">Dataset with header</option>
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91 <option value="with_rownames">Dataset with row names</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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92 <option value="with_header_rownames">Dataset with header and row names</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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93 <option value="no_header_rownames">Dataset without header or row names</option>
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94 </param>
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95 <when value="with_header">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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96 <param name="header" type="hidden" value="TRUE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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97 <param name="row_names_index" type="hidden" value="0"/>
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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">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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99 <option value="TRUE" selected="true">horizontal</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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100 <option value="FALSE">vertial</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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101 </param>
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102 </when>
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103 <when value="with_rownames">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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104 <param name="header" type="hidden" value="FALSE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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106 <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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107 <option value="TRUE">horizontal</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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108 <option value="FALSE" selected="true">vertial</option>
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109 </param>
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110 </when>
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diff changeset
111 <when value="with_header_rownames">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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112 <param name="header" type="hidden" value="TRUE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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115 <option value="TRUE" selected="true">horizontal</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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116 <option value="FALSE">vertial</option>
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diff changeset
117 </param>
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118 </when>
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119 <when value="no_header_rownames">
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diff changeset
120 <param name="header" type="hidden" value="FALSE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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121 <param name="row_names_index" type="hidden" value="0"/>
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diff changeset
122 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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123 </when>
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124 </conditional>
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diff changeset
125 </xml>
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126 <xml name="transform">
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127 <param name="transform" type="select" label="Data transformation">
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128 <option value="none">Plot the data as it is</option>
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129 <option value="log2">Log2(value) transform my data</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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130 <option value="log2plus1">Log2(value+1) transform my data</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
131 <option value="log10">Log10(value) transform my data</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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132 <option value="log10plus1">Log10(value+1) transform my data</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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133 </param>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
134 </xml>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
135 <xml name="xy_scaling">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
136 <conditional name="scaling">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
137 <param name="plot_scaling" type="select" label="Axis scaling">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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138 <option value="Automatic" selected="true">Automatic axis scaling</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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139 <option value="Defined">User-defined axis scales</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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140 </param>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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parents: 4
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141 <when value="Automatic"/>
0
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142 <when value="Defined">
2
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143 <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
de981b15693a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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parents: 0
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144 <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
de981b15693a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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parents: 0
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145 <param name="yaxismin" type="float" value="0" label="minimal range of y-axis" />
de981b15693a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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parents: 0
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146 <param name="yaxismax" type="float" value="3" label="maximal range of y-axis" />
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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147 </when>
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148 </conditional>
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diff changeset
149 </xml>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
150 <xml name="title">
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151 <param name="title" type="text" value="" label="Plot title">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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152 <!--<sanitizer sanitize="false"/> -->
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 </param>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
154 </xml>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
155 <xml name="xy_lab">
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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parents: 4
diff changeset
156 <param name="xlab" type="text" value="Title of x-axis" label="Label for x axis">
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
157 <sanitizer sanitize="false"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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158 </param>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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diff changeset
159 <param name="ylab" type="text" value="Title of y-axis" label="Label for y axis">
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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160 <sanitizer sanitize="false"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
161 </param>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
162 </xml>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
163 <xml name="legend">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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164 <param name="legend" type="select" label="Legend options">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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165 <option value="yes">Include legend on plot</option>
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166 <option value="no">Hide legend</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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167 </param>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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168 </xml>
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169 <xml name="theme">
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170 <param name="theme" type="select" label="Backgound theme for plot">
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171 <option value="bw">Black and white</option>
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172 <option value="Default">Default (grey)</option>
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173 </param>
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174 </xml>
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175 <xml name="dimensions">
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176 <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="Default: inches.">
0
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177 <option value="in" selected="true">Inches (in)</option>
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178 <option value="cm">Centimeters (cm)</option>
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179 <option value="mm">Millimeters (mm)</option>
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180 </param>
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181 <param name="width_output_dim" type="float" value="7" label="width of output"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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182 <param name="height_output_dim" type="float" value="7" label="height of output"/>
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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."/>
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184 <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format.">
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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185 <option value="none" selected="true">Only PNG</option>
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186 <option value="pdf">PDF</option>
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187 <option value="svg">SVG</option>
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188 <option value="eps">EPS</option>
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189 <option value="ps">PS</option>
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190 <option value="tex">TEX (pictex)</option>
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191 <option value="jpeg">JPEG</option>
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192 <option value="tiff">TIFF</option>
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193 <option value="bmp">BMP</option>
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194 </param>
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195 </xml>
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diff changeset
196 <xml name="citations">
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diff changeset
197 <citations>
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198 <citation type="bibtex">@book{wickham2009ggplot2,
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199 author = {Hadley Wickham},
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200 title = {ggplot2: Elegant Graphics for Data Analysis},
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201 publisher = {Springer-Verlag New York},
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202 year = {2009},
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203 isbn = {978-0-387-98140-6},
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204 url = {https://ggplot2.tidyverse.org/},
0
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205 }
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206 </citation>
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diff changeset
207 <yield />
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208 </citations>
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209 </xml>
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210 <xml name="axis_customization" token_label="Axis title options">
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211 <param name="axis_customization" type="select" label="@LABEL@">
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212 <option value="default" selected="true">Default</option>
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213 <option value="defined">User defined label options</option>
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214 </param>
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diff changeset
215 <when value="default"/>
0
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diff changeset
216 <when value="defined">
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217 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
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218 <param name="color" type="select" label="Color of axis label">
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219 <option value="black">Black (default)</option>
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220 <option value="red">Red</option>
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221 <option value="white">White</option>
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222 <option value="blue">Blue</option>
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223 <option value="orange">Orange</option>
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224 <option value="yellow">Yellow</option>
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225 <option value="green">Green</option>
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226 <option value="purple">Purple</option>
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227 <option value="magenta">Magenta</option>
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228 <option value="cyan">Cyan</option>
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229 <option value="grey">Grey</option>
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230 <option value="gold">Gold</option>
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231 </param>
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232 <param name="face" type="select" label="Font effect of axis label">
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233 <option value="plain">Normal (default)</option>
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234 <option value="bold">Bold</option>
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235 <option value="italic">Italic</option>
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236 </param>
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237 </when>
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238 </xml>
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239 <xml name="colors">
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240 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
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241 <option value="Default">Default color scheme</option>
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242 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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243 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
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244 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
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245 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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246 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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247 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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248 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
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249 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
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250 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
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251 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
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252 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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253 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
254 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
255 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
256 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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257 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
258 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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259 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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260 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
261 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
262 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
263 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
264 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
265 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
266 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
267 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
268 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
269 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
270 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
271 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
272 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
273 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
274 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
275 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
276 </param>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
277 </xml>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
278 <xml name="additional_output">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
279 <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
280 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
281 <change_format>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
282 <when input="out.additional_output_format" value="svg" format="svg" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
283 <when input="out.additional_output_format" value="eps" format="eps" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
284 <when input="out.additional_output_format" value="ps" format="ps" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
285 <when input="out.additional_output_format" value="tex" format="txt" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
286 <when input="out.additional_output_format" value="jpeg" format="jpg" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
287 <when input="out.additional_output_format" value="tiff" format="tiff" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
288 <when input="out.additional_output_format" value="bmp" format="bmp" />
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
289 </change_format>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
290 <filter>out['additional_output_format'] != "none"</filter>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
291 </data>
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
292 </xml>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
293 <xml name="points_options">
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
294 <conditional name="points">
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
295 <param name="pointoptions" type="select" label="Data point options">
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
296 <option value="default" selected="true">Default</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
297 <option value="defined">User defined point options</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
298 </param>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
299 <when value="default">
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
300 <!--Do nothing here -->
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
301 </when>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
302 <when value="defined">
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
303 <param name="size" type="float" value="1" label="relative size of points" />
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
304 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
305 <param name="pointcolor" type="select" label="Color of data points" >
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
306 <option value="black">Black (default)</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
307 <option value="red">Red</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
308 <option value="white">White</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
309 <option value="blue">Blue</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
310 <option value="orange">Orange</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
311 <option value="yellow">Yellow</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
312 <option value="green">Green</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
313 <option value="purple">Purple</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
314 <option value="magenta">Magenta</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
315 <option value="cyan">Cyan</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
316 <option value="grey">Grey</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
317 <option value="gold">Gold</option>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 4
diff changeset
318 </param>
6
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
319 <param name="shape" type="select" label="Shape of data points" >
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
320 <option value="0">square</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
321 <option value="1">circle</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
322 <option value="2">triangle point up</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
323 <option value="3">plus</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
324 <option value="4">cross</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
325 <option value="5">diamond</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
326 <option value="6">triangle point down</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
327 <option value="7">square cross</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
328 <option value="8">star</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
329 <option value="9">diamond plus</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
330 <option value="10">circle plus</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
331 <option value="11">triangles up and down</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
diff changeset
332 <option value="12">square plus</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
parents: 5
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333 <option value="13">circle cross</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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334 <option value="14">square and triangle down</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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335 <option value="15">filled square</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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336 <option value="16">filled circle</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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337 <option value="17">filled triangle point-up</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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338 <option value="18">filled diamond</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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339 <option value="19">solid circle</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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340 <option value="20">bullet (smaller circle)</option>
3f13d3158bf5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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341 </param>
5
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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342 </when>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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343 </conditional>
f6f9f2ec14bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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344 </xml>
8
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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345 <xml name="data_input">
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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346 <param name="input_data" type="data" format="csv,tsv,txt,tabular,parquet" label="Input table" help= "Input file in a tabular/tsv/csv/parquet format"/>
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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347 </xml>
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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348
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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349 <xml name="axes_labels">
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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350 <param name="xlab" type="text" label="Label for the x axis" optional="true"/>
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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351 <param name="ylab" type="text" label="Label for the y axis" optional="true"/>
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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352 </xml>
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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353
8b8a26a5fdf2 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">
8b8a26a5fdf2 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"
8b8a26a5fdf2 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."/>
8b8a26a5fdf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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357 </xml>
0
d9b2b499a9dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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358 </macros>