Mercurial > repos > iuc > ggplot2_histogram

annotate macros.xml @ 13:6b9816a913de draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
author iuc
date Thu, 15 May 2025 13:02:22 +0000
parents 6fc8bab811da
children
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9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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1 <?xml version="1.0"?>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
8
355a82227003 "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>
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9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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6 <yield />
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7 </requirements>
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8 </xml>
7
398e5104f8a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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9 <xml name="bio_tools">
398e5104f8a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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10 <xrefs>
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11 <xref type="bio.tools">ggplot2</xref>
7
398e5104f8a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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12 </xrefs>
398e5104f8a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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13 </xml>
13
6b9816a913de 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>
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6fc8bab811da 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>
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9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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17 <token name="@R_INIT@"><![CDATA[
2
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18 ## Setup R error handling to go to stderr
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19 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
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20
2
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21 ## Unify locale settings
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22 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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23 ]]></token>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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25 <token name="@TRANSFORM@"><![CDATA[
2
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26 #if $adv.transform == "log2"
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27 input["value"] <- log2(input["value"])
f52035800250 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"
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29 input["value"] <- log2(input["value"]+1)
f52035800250 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"
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31 input["value"] <- log10(input["value"])
f52035800250 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"
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33 input["value"] <- log10(input["value"]+1)
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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34 #end if
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35 ]]></token>
f52035800250 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[
f52035800250 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
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39 #if $adv.scaling.plot_scaling == "Automatic"
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 gg_scalex = NULL
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41 gg_scaley = NULL
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42 #else
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43 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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44 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
f52035800250 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)
f52035800250 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)
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47 cat("\n yaxismin: ", $adv.scaling.yaxismin)
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48 cat("\n yaxismax: ", $adv.scaling.yaxismax)
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49 #end if
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50 ]]></token>
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51
f52035800250 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[
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53 ## Choose theme for plot
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54 #if $adv.theme == "bw"
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55 gg_theme = theme_bw()
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56 #else
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57 gg_theme = NULL
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58 #end if
0
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59 ]]></token>
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60
2
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61 <token name="@LEGEND@"><![CDATA[
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62 ## Show/hide legend
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63 #if $adv.legend == "yes"
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64 gg_legend = theme(legend.position="right")
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65 #else
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66 gg_legend = theme(legend.position="none")
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67 cat("\n no legend")
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68 #end if
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69 ]]></token>
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70 <token name="@SAVE_OUTPUT@"><![CDATA[
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71 ## output options need to be in out section
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72 gg_width <- as.double('$out.width_output_dim')
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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('$out.dpi_output_dim')
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76 gg_add_device <- '$out.additional_output_format'
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77 output1 <- '$output1'
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78 output2 <- '$output2'
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79
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80 ## ggsave to png
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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"){
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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)
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84 }
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85 ]]></token>
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86 <xml name="read_complex_input">
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87 <param name="input1" type="data" format="tabular" label="Select table"/>
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parents: 0
diff changeset
88 <conditional name="inputdata">
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parents: 0
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89 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
f52035800250 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 <option value="with_header" selected="true">Dataset with header</option>
f52035800250 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 <option value="with_rownames">Dataset with row names</option>
f52035800250 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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92 <option value="with_header_rownames">Dataset with header and row names</option>
f52035800250 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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93 <option value="no_header_rownames">Dataset without header or row names</option>
f52035800250 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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94 </param>
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parents: 0
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95 <when value="with_header">
f52035800250 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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96 <param name="header" type="hidden" value="TRUE"/>
f52035800250 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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97 <param name="row_names_index" type="hidden" value="0"/>
f52035800250 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="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names">
f52035800250 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>
f52035800250 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>
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parents: 0
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101 </param>
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102 </when>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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103 <when value="with_rownames">
f52035800250 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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104 <param name="header" type="hidden" value="FALSE"/>
f52035800250 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"/>
f52035800250 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">
f52035800250 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>
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108 <option value="FALSE" selected="true">vertial</option>
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109 </param>
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110 </when>
f52035800250 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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111 <when value="with_header_rownames">
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
diff changeset
112 <param name="header" type="hidden" value="TRUE"/>
f52035800250 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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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"/>
f52035800250 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">
f52035800250 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>
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116 <option value="FALSE">vertial</option>
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117 </param>
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118 </when>
f52035800250 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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119 <when value="no_header_rownames">
f52035800250 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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120 <param name="header" type="hidden" value="FALSE"/>
f52035800250 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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121 <param name="row_names_index" type="hidden" value="0"/>
f52035800250 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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122 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
f52035800250 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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123 </when>
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124 </conditional>
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125 </xml>
0
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126 <xml name="transform">
2
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127 <param name="transform" type="select" label="Data transformation">
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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130 <option value="log2plus1">Log2(value+1) transform my data</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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131 <option value="log10">Log10(value) transform my data</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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132 <option value="log10plus1">Log10(value+1) transform my data</option>
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133 </param>
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134 </xml>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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135 <xml name="xy_scaling">
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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136 <conditional name="scaling">
2
f52035800250 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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137 <param name="plot_scaling" type="select" label="Axis scaling">
f52035800250 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>
f52035800250 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>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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140 </param>
8
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141 <when value="Automatic"/>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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142 <when value="Defined">
4
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143 <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
1f0242e49a58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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144 <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
1f0242e49a58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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145 <param name="yaxismin" type="float" value="0" label="minimal range of y-axis" />
1f0242e49a58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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146 <param name="yaxismax" type="float" value="3" label="maximal range of y-axis" />
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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147 </when>
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148 </conditional>
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149 </xml>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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150 <xml name="title">
2
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151 <param name="title" type="text" value="" label="Plot title">
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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152 <!--<sanitizer sanitize="false"/> -->
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153 </param>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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154 </xml>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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155 <xml name="xy_lab">
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156 <param name="xlab" type="text" value="Title of x-axis" label="Label for x axis">
2
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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157 <sanitizer sanitize="false"/>
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158 </param>
8
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159 <param name="ylab" type="text" value="Title of y-axis" label="Label for y axis">
2
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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160 <sanitizer sanitize="false"/>
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161 </param>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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162 </xml>
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163 <xml name="legend">
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164 <param name="legend" type="select" label="Legend options">
f52035800250 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>
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167 </param>
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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>
0
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diff changeset
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.">
2
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177 <option value="in" selected="true">Inches (in)</option>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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178 <option value="cm">Centimeters (cm)</option>
f52035800250 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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179 <option value="mm">Millimeters (mm)</option>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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180 </param>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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181 <param name="width_output_dim" type="float" value="7" label="width of output"/>
f52035800250 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"/>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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.">
355a82227003 "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>
2
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parents: 0
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186 <option value="pdf">PDF</option>
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187 <option value="svg">SVG</option>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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191 <option value="jpeg">JPEG</option>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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192 <option value="tiff">TIFF</option>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents: 0
diff changeset
193 <option value="bmp">BMP</option>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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194 </param>
0
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195 </xml>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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196 <xml name="citations">
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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diff changeset
197 <citations>
2
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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198 <citation type="bibtex">@book{wickham2009ggplot2,
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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199 author = {Hadley Wickham},
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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200 title = {ggplot2: Elegant Graphics for Data Analysis},
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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201 publisher = {Springer-Verlag New York},
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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202 year = {2009},
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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203 isbn = {978-0-387-98140-6},
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497d700a5229 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 8e0f13edc2c06772dac0c1258e362045e68028b8"
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204 url = {https://ggplot2.tidyverse.org/},
0
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205 }
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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206 </citation>
2
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207 <yield />
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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208 </citations>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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209 </xml>
2
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210 <xml name="axis_customization" token_label="Axis title options">
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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211 <param name="axis_customization" type="select" label="@LABEL@">
2
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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212 <option value="default" selected="true">Default</option>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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213 <option value="defined">User defined label options</option>
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214 </param>
8
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diff changeset
215 <when value="default"/>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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)"/>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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218 <param name="color" type="select" label="Color of axis label">
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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219 <option value="black">Black (default)</option>
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220 <option value="red">Red</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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>
2
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230 <option value="gold">Gold</option>
0
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diff changeset
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>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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243 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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244 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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245 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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246 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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247 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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248 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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249 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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250 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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diff changeset
251 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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252 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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253 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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254 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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255 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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256 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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257 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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258 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
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259 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
260 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
261 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
262 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
263 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
264 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
265 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
266 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
267 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
268 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
269 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
270 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
271 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
272 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
273 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
274 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
2
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
275 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
276 </param>
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
277 </xml>
2
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
278 <xml name="additional_output">
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
279 <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
280 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
281 <change_format>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
282 <when input="out.additional_output_format" value="svg" format="svg" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
283 <when input="out.additional_output_format" value="eps" format="eps" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
284 <when input="out.additional_output_format" value="ps" format="ps" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
285 <when input="out.additional_output_format" value="tex" format="txt" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
286 <when input="out.additional_output_format" value="jpeg" format="jpg" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
287 <when input="out.additional_output_format" value="tiff" format="tiff" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
288 <when input="out.additional_output_format" value="bmp" format="bmp" />
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
289 </change_format>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
290 <filter>out['additional_output_format'] != "none"</filter>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
291 </data>
f52035800250 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 0
diff changeset
292 </xml>
8
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
293 <xml name="points_options">
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
294 <conditional name="points">
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
295 <param name="pointoptions" type="select" label="Data point options">
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
296 <option value="default" selected="true">Default</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
297 <option value="defined">User defined point options</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
298 </param>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
299 <when value="default">
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
300 <!--Do nothing here -->
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
301 </when>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
302 <when value="defined">
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
303 <param name="size" type="float" value="1" label="relative size of points" />
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
304 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" />
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
305 <param name="pointcolor" type="select" label="Color of data points" >
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
306 <option value="black">Black (default)</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
307 <option value="red">Red</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
308 <option value="white">White</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
309 <option value="blue">Blue</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
310 <option value="orange">Orange</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
311 <option value="yellow">Yellow</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
312 <option value="green">Green</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
313 <option value="purple">Purple</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
314 <option value="magenta">Magenta</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
315 <option value="cyan">Cyan</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
316 <option value="grey">Grey</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
317 <option value="gold">Gold</option>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
318 </param>
9
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
319 <param name="shape" type="select" label="Shape of data points" >
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
320 <option value="0">square</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
321 <option value="1">circle</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
322 <option value="2">triangle point up</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
323 <option value="3">plus</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
324 <option value="4">cross</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
325 <option value="5">diamond</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
326 <option value="6">triangle point down</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
327 <option value="7">square cross</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
328 <option value="8">star</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
329 <option value="9">diamond plus</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
330 <option value="10">circle plus</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
331 <option value="11">triangles up and down</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
332 <option value="12">square plus</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
333 <option value="13">circle cross</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
334 <option value="14">square and triangle down</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
335 <option value="15">filled square</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
336 <option value="16">filled circle</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
337 <option value="17">filled triangle point-up</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
338 <option value="18">filled diamond</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
339 <option value="19">solid circle</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
340 <option value="20">bullet (smaller circle)</option>
fb50ab943396 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents: 8
diff changeset
341 </param>
8
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
342 </when>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
343 </conditional>
355a82227003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents: 7
diff changeset
344 </xml>
13
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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345 <xml name="data_input">
6b9816a913de 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"/>
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents: 12
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347 </xml>
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents: 12
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348
6b9816a913de 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">
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents: 12
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350 <param name="xlab" type="text" label="Label for the x axis" optional="true"/>
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents: 12
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351 <param name="ylab" type="text" label="Label for the y axis" optional="true"/>
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents: 12
diff changeset
352 </xml>
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
parents: 12
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353
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents: 12
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354 <xml name="export_data">
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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parents: 12
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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"
6b9816a913de 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."/>
6b9816a913de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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357 </xml>
0
9d060114554c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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358 </macros>