Mercurial > repos > iuc > ggplot2_barplot

annotate ggplot2_barplot.xml @ 0:f098df64f6ad draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
author iuc
date Thu, 15 May 2025 13:00:48 +0000
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f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
iuc
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1 <tool id="ggplot2_barplot" name="Barplot w ggplot2" version="@TOOL_VERSION@+galaxy0" profile="23.0">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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2 <description>Barplot visualization tool using ggplot2</description>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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3 <macros>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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4 <import>macros.xml</import>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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5 </macros>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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6 <expand macro="requirements">
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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7 <requirement type="package" version="1.3.1">r-tidyr</requirement>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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8 <requirement type="package" version="19.0.0">r-arrow</requirement>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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9 <requirement type="package" version="1.1.5">r-rlang</requirement>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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10 </expand>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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11 <required_files>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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12 <include path="utils.r" />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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13 </required_files>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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14 <creator>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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15 <person
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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16 givenName="Kristina"
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17 familyName="Gomoryova"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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18 url="https://github.com/KristinaGomoryova"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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19 identifier="0000-0003-4407-3917" />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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20 <person
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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21 givenName="Helge"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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22 familyName="Hecht"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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23 url="https://github.com/hechth"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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24 identifier="0000-0001-6744-996X" />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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25 <organization
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26 url="https://www.recetox.muni.cz/"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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27 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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28 name="RECETOX MUNI" />
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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29 </creator>
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30
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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31 <command detect_errors="exit_code"><![CDATA[
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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32 Rscript -e 'source("${__tool_directory__}/utils.r")' -e 'source("${run_script}")'
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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33 #if $export_R_script
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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34 && cat ${run_script} >> $script
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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35 #end if
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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36 ]]></command>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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37
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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38 <configfiles>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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39 <configfile name="run_script"><![CDATA[
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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40 file_name <- "$input_data"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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41 file_extension <- "$input_data.ext"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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42 data_input <- load_data(file_name, file_extension)
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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43
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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44 quant_col <- colnames(data_input)[$quant_col]
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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45 grouping_col <- colnames(data_input)[$grouping_col]
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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46 data_input[[grouping_col]] <- as.factor(data_input[[grouping_col]])
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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47
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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48 #if $color_col
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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49 color_col <- colnames(data_input)[$color_col]
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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50 data_input[[color_col]] <- as.factor(data_input[[color_col]])
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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51 #end if
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52
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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53 plot_barplot <- ggplot2::ggplot(data_input,
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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54 ggplot2::aes(x = !!rlang::sym(grouping_col),
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55 y = !!rlang::sym(quant_col),
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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56 #if $color_col
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57 fill = !!rlang::sym(color_col)
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58 #end if
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59 )) +
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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60 ggplot2::geom_bar(stat="identity"
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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61 #if $position
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62 , position = ggplot2::position_dodge()
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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63 #end if
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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64 ) +
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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65 ggplot2::theme_bw()+
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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66 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust=1))
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67
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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68 #if $xlab
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69 plot_barplot <- plot_barplot + ggplot2::xlab("$xlab")
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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70 #end if
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71
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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72 #if $ylab
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73 plot_barplot <- plot_barplot + ggplot2::ylab("$ylab")
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74 #end if
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75
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76 ggplot2::ggsave(filename = "barplot.png", plot_barplot)
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77
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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78 ]]></configfile>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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79 </configfiles>
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80
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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81 <inputs>
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82 <param name="input_data" type="data" format="csv,tsv,txt,tabular,parquet" label="Input table in a long format" help= "Input file in a tabular/tsv/csv/parquet format"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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83 <param name="quant_col" type="data_column" data_ref="input_data" use_header_names="true" label="Which column contains the quantitative information?" help="Select the column containing quantitative information."/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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84 <param name="grouping_col" type="data_column" data_ref="input_data" use_header_names="true" label="Which column contains the categories?" help="Select the column which contains the categories."/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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85 <param name="color_col" type="data_column" data_ref="input_data" use_header_names="true" optional="true" label="Which column to color according to?" help="Select the column which contains levels for color."/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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86 <param name="position" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use position dodge?" help="If a column for color is specified, should be the categories placed side-by-side or stacked (default)?"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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87 <expand macro="axes_labels"/>
f098df64f6ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
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88 <expand macro="export_data"/>
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89 </inputs>
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90
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91 <outputs>
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92 <data name="barplot" format="png" label="Barplot on ${on_string}" from_work_dir="barplot.png"/>
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93 <data name="script" format="txt" label="R script">
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94 <filter>export_R_script</filter>
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95 </data>
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96 </outputs>
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97
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98 <tests>
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99 <test expect_num_outputs="1">
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100 <param name="input_data" value="barplot_test_data.txt"/>
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101 <param name="quant_col" value="3"/>
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102 <param name="grouping_col" value="4"/>
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103 <output name="barplot" ftype="png">
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104 <assert_contents>
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105 <has_image_channels channels="1"/>
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106 <has_image_height height="2100"/>
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107 <has_image_width width="2100" />
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108 <has_image_center_of_mass center_of_mass="1030.12, 1008.25" eps="0.1"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112 </tests>
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113
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114 <help><![CDATA[
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115 recetox-barplot help
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116 =====================
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117
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118 Overview
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119 --------
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120
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121 recetox-barplot allows creating barplots from tabular/csv/parquet data. On the input, data in a long format are expected, meaning that each column represents a variable, each row represents an observation as shown below.
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122
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123 User has to define which column holds the quantitative information (e.g. counts for particular category) and which column contains the categories to be plotted. It is also possible to use another variable to color the bars. Finally, `Use position dodge?` parameter defines whether the bars will be stacked above each other (default behavior when set to FALSE) or will be placed side-by-side (when set to TRUE). If no color column is supplied, setting this parameter will have no effect on the resulting barplots.
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124
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125 Example barplot input
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126 ----------------------
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127
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128 +----------------------+-------------------+-----------------------+--------------------+
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129 | SampleName | replicate | condition | Value |
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130 +======================+===================+=======================+====================+
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131 | sample1 | 1 | control | 20 |
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132 +----------------------+-------------------+-----------------------+--------------------+
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133 | sample2 | 1 | treatment | 40 |
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134 +----------------------+-------------------+-----------------------+--------------------+
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135 | sample3 | 2 | treatment | 10 |
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136 +----------------------+-------------------+-----------------------+--------------------+
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137 | ... | ... | ... | ... |
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138 +----------------------+-------------------+-----------------------+--------------------+
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139 ]]></help>
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140
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141 <expand macro="citations" />
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142 </tool>