Mercurial > repos > iuc > ggplot2_violin

annotate macros.xml @ 2:43778344b955 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
author iuc
date Mon, 11 Jun 2018 16:05:43 -0400
parents a597d59df9ee
children 637cf21db396
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a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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1 <?xml version="1.0"?>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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2 <macros>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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3 <xml name="requirements">
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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4 <requirements>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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5 <requirement type="package" version="@VERSION@">r-ggplot2</requirement>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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6 <yield />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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7 </requirements>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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8 </xml>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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9 <token name="@VERSION@">2.2.1</token>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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11 <token name="@R_INIT@"><![CDATA[
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43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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12 ## Setup R error handling to go to stderr
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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13 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
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a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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14
2
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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15 ## Unify locale settings
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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16 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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17 ]]></token>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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19 <token name="@TRANSFORM@"><![CDATA[
2
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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20 #if $adv.transform == "log2"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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21 input["value"] <- log2(input["value"])
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22 #elif $adv.transform == "log2plus1"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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23 input["value"] <- log2(input["value"]+1)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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24 #elif $adv.transform == "log10"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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25 input["value"] <- log10(input["value"])
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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26 #elif $adv.transform == "log10plus1"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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27 input["value"] <- log10(input["value"]+1)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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28 #end if
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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29 ]]></token>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 <token name="@XY_SCALING@"><![CDATA[
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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32 #Choose between automatically scaled x and y axis or user defined
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33 #if $adv.scaling.plot_scaling == "Automatic"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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34 gg_scalex = NULL
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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35 gg_scaley = NULL
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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36 #else
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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37 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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38 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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39 cat("\n xaxismin: ", $adv.scaling.xaxismin)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 cat("\n xaxismax: ", $adv.scaling.xaxismax)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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41 cat("\n yaxismin: ", $adv.scaling.yaxismin)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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42 cat("\n yaxismax: ", $adv.scaling.yaxismax)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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43 #end if
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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44 ]]></token>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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45
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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46 <token name="@THEME@"><![CDATA[
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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47 ## Choose theme for plot
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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48 #if $adv.theme == "bw"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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49 gg_theme = theme_bw()
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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50 #else
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51 gg_theme = NULL
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52 #end if
0
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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53 ]]></token>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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54
2
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55 <token name="@LEGEND@"><![CDATA[
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56 ## Show/hide legend
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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57 #if $adv.legend == "yes"
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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58 gg_legend = theme(legend.position="right")
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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59 #else
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60 gg_legend = theme(legend.position="none")
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61 cat("\n no legend")
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62 #end if
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63 ]]></token>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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64 <token name="@SAVE_OUTPUT@"><![CDATA[
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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65 ## output options need to be in out section
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66 gg_width <- as.double('$out.width_output_dim')
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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67 gg_height <- as.double('$out.height_output_dim')
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68 gg_unit <- '$out.unit_output_dim'
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69 gg_dpi <- as.double('$out.dpi_output_dim')
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70 gg_add_device <- '$out.additional_output_format'
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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71 output1 <- '$output1'
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72 output2 <- '$output2'
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73
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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74 ## ggsave to png
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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75 ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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76 if(gg_add_device != "none"){
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77 ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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78 }
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79 ]]></token>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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80 <xml name="read_complex_input">
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81 <param name="input1" type="data" format="tabular" label="Select table"/>
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82 <conditional name="inputdata">
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83 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
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84 <option value="with_header" selected="true">Dataset with header</option>
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85 <option value="with_rownames">Dataset with row names</option>
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86 <option value="with_header_rownames">Dataset with header and row names</option>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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87 <option value="no_header_rownames">Dataset without header or row names</option>
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88 </param>
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89 <when value="with_header">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
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90 <param name="header" type="hidden" value="TRUE"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
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91 <param name="row_names_index" type="hidden" value="0"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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92 <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">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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93 <option value="TRUE" selected="true">horizontal</option>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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94 <option value="FALSE">vertial</option>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
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95 </param>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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96 </when>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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97 <when value="with_rownames">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
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98 <param name="header" type="hidden" value="FALSE"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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99 <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"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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100 <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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101 <option value="TRUE">horizontal</option>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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102 <option value="FALSE" selected="true">vertial</option>
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103 </param>
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104 </when>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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105 <when value="with_header_rownames">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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106 <param name="header" type="hidden" value="TRUE"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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107 <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"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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108 <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">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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109 <option value="TRUE" selected="true">horizontal</option>
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110 <option value="FALSE">vertial</option>
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111 </param>
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112 </when>
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113 <when value="no_header_rownames">
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114 <param name="header" type="hidden" value="FALSE"/>
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115 <param name="row_names_index" type="hidden" value="0"/>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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116 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
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117 </when>
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118 </conditional>
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119 </xml>
0
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120 <xml name="transform">
2
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121 <param name="transform" type="select" label="Data transformation">
0
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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122 <option value="none">Plot the data as it is</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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123 <option value="log2">Log2(value) transform my data</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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124 <option value="log2plus1">Log2(value+1) transform my data</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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125 <option value="log10">Log10(value) transform my data</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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126 <option value="log10plus1">Log10(value+1) transform my data</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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127 </param>
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128 </xml>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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129 <xml name="xy_scaling">
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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130 <conditional name="scaling">
2
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131 <param name="plot_scaling" type="select" label="Axis scaling">
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132 <option value="Automatic" selected="true">Automatic axis scaling</option>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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133 <option value="Defined">User-defined axis scales</option>
0
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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134 </param>
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135 <when value="Automatic">
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136 <!--Do nothing here -->
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137 </when>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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138 <when value="Defined">
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139 <param name="xaxismin" type="integer" value="0" label="minimal range of x-axis" />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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140 <param name="xaxismax" type="integer" value="3" label="maximal range of x-axis" />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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141 <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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142 <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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143 </when>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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144 </conditional>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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145 </xml>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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146 <xml name="title">
2
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147 <param name="title" type="text" value="" label="Plot title">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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148 <!--<sanitizer sanitize="false"/> -->
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149 </param>
0
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150 </xml>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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151 <xml name="xy_lab">
2
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152 <param name="xlab" type="text" value="title of x-axis" label="Label for x axis">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 <sanitizer sanitize="false"/>
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154 </param>
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155 <param name="ylab" type="text" value="title of y-axis" label="Label for y axis">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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156 <sanitizer sanitize="false"/>
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157 </param>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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158 </xml>
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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159 <xml name="legend">
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160 <param name="legend" type="select" label="Legend options">
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161 <option value="yes">Include legend on plot</option>
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162 <option value="no">Hide legend</option>
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163 </param>
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164 </xml>
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165 <xml name="theme">
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166 <param name="theme" type="select" label="Backgound theme for plot">
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167 <option value="bw">Black and white</option>
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168 <option value="Default">Default (grey)</option>
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169 </param>
0
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170 </xml>
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171 <xml name="dimensions">
2
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172 <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="default inches">
43778344b955 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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173 <option value="in" selected="true">Inches (in)</option>
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174 <option value="cm">Centimeters (cm)</option>
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175 <option value="mm">Millimeters (mm)</option>
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176 </param>
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177 <param name="width_output_dim" type="float" value="7" label="width of output"/>
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178 <param name="height_output_dim" type="float" value="7" label="height of output"/>
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179 <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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180 <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format">
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181 <option value="none" selected="true">only PNG</option>
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182 <option value="pdf">PDF</option>
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183 <option value="svg">SVG</option>
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184 <option value="eps">EPS</option>
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185 <option value="ps">PS</option>
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186 <option value="tex">TEX (pictex)</option>
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187 <option value="jpeg">JPEG</option>
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188 <option value="tiff">TIFF</option>
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189 <option value="bmp">BMP</option>
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190 </param>
0
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191 </xml>
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192 <xml name="citations">
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193 <citations>
2
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194 <citation type="bibtex">@book{wickham2009ggplot2,
0
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195 author = {Hadley Wickham},
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196 title = {ggplot2: Elegant Graphics for Data Analysis},
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197 publisher = {Springer-Verlag New York},
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198 year = {2009},
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199 isbn = {978-0-387-98140-6},
2
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200 url = {http://ggplot2.org},
0
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201 }
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202 </citation>
2
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203 <yield />
0
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204 </citations>
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205 </xml>
2
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206 <xml name="axis_customization" token_label="Axis title options">
0
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207 <param name="axis_customization" type="select" label="@LABEL@">
2
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208 <option value="default" selected="true">Default</option>
0
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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209 <option value="defined">User defined label options</option>
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210 </param>
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211 <when value="default">
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212 <!--Do nothing here -->
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213 </when>
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214 <when value="defined">
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215 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
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216 <param name="color" type="select" label="Color of axis label">
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217 <option value="black">Black (default)</option>
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218 <option value="red">Red</option>
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219 <option value="white">White</option>
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220 <option value="blue">Blue</option>
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221 <option value="orange">Orange</option>
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222 <option value="yellow">Yellow</option>
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223 <option value="green">Green</option>
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224 <option value="purple">Purple</option>
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225 <option value="magenta">Magenta</option>
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226 <option value="cyan">Cyan</option>
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227 <option value="grey">Grey</option>
2
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228 <option value="gold">Gold</option>
0
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229 </param>
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230 <param name="face" type="select" label="Font effect of axis label">
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231 <option value="plain">Normal (default)</option>
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232 <option value="bold">Bold</option>
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233 <option value="italic">Italic</option>
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234 </param>
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235 </when>
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236 </xml>
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237 <xml name="colors">
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238 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
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239 <option value="Default">Default color scheme</option>
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240 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
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241 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
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242 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
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243 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
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244 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
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245 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
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246 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
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247 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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248 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
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249 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
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250 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
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251 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
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252 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
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253 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
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254 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
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255 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
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256 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
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257 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
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258 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
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259 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
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260 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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261 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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262 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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263 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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264 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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265 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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266 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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267 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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268 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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269 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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270 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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271 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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272 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
2
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273 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
0
a597d59df9ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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274 </param>
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275 </xml>
2
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276 <xml name="additional_output">
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277 <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
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278 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
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279 <change_format>
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280 <when input="out.additional_output_format" value="svg" format="svg" />
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281 <when input="out.additional_output_format" value="eps" format="eps" />
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282 <when input="out.additional_output_format" value="ps" format="ps" />
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283 <when input="out.additional_output_format" value="tex" format="txt" />
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284 <when input="out.additional_output_format" value="jpeg" format="jpg" />
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285 <when input="out.additional_output_format" value="tiff" format="tiff" />
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286 <when input="out.additional_output_format" value="bmp" format="bmp" />
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287 </change_format>
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288 <filter>out['additional_output_format'] != "none"</filter>
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289 </data>
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290 </xml>
0
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291 </macros>