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20
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1 <tool id="charts" name="Charts" version="1.0.0">
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2 <hidden>True</hidden>
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3 <description>wrapper for R</description>
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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56
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6 <requirement type="package" version="3.0.3">R</requirement>
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62
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7 <requirement type="package" version="1.0">charts_r_packages</requirement>
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20
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8 </requirements>
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9 <command>Rscript \$SCRIPT_PATH/charts.r -w \$SCRIPT_PATH/ -m ${module} -i ${input} -c '${columns}' -s '${settings}' -o ${output}
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10 </command>
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11 <inputs>
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12 <param name="input" type="data" label="Input dataset" format="tabular" />
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13 <param name="module" type="select" label="R-script">
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33
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14 <option value="boxplot">boxplot</option>
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15 <option value="heatmap">heatmap</option>
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16 <option value="histogram">histogram</option>
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17 <option value="histogramdiscrete">histogramdiscrete</option>
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20
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18 </param>
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66
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19 <param name="columns" type="text" area="true" label="Columns string (i.e key1: column, key2: column)" value="column: 2"/>
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20 <param name="settings" type="text" area="true" label="Options string (i.e data_limit: 1000)" value=""/>
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20
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="tabular" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" value="tabular.txt" />
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28 <param name="module" value="histogram" />
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29 <param name="columns" value="key1: 2" />
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30 <param name="settings" value="" />
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31 <output name="output" file="histogram.000.txt" lines_diff="2"/>
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32 </test>
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33 <test>
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34 <param name="input" value="tabular.txt" />
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35 <param name="module" value="histogram" />
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36 <param name="columns" value="key1: 2, key2: 3, key3: 4" />
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37 <param name="settings" value="" />
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38 <output name="output" file="histogram.001.txt" lines_diff="2"/>
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39 </test>
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40 <test>
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54
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41 <param name="input" value="tabular_data.txt" />
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42 <param name="module" value="histogram" />
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43 <param name="columns" value="key1: 6" />
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44 <param name="settings" value="" />
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45 <output name="output" file="histogram.002.txt" lines_diff="2"/>
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46 </test>
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47 <test>
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48
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48 <param name="input" value="tabular_single.txt" />
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49 <param name="module" value="histogram" />
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50 <param name="columns" value="key1: 1" />
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51 <param name="settings" value="" />
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52 <output name="output" file="histogram.003.txt" lines_diff="2"/>
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53 </test>
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54 <test>
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55 <param name="input" value="tabular.txt" />
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56 <param name="module" value="boxplot" />
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57 <param name="columns" value="key1: 2" />
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58 <param name="settings" value="" />
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59 <output name="output" file="boxplot.000.txt" lines_diff="2"/>
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60 </test>
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61 <test>
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62 <param name="input" value="tabular.txt" />
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63 <param name="module" value="boxplot" />
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64 <param name="columns" value="key1: 2, key2: 3, key3: 4" />
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65 <param name="settings" value="" />
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66 <output name="output" file="boxplot.001.txt" lines_diff="2"/>
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67 </test>
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33
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68 <test>
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69 <param name="input" value="tabular_matrix.txt" />
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70 <param name="module" value="histogramdiscrete" />
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71 <param name="columns" value="key1: 1, key2: 2, key3: 3" />
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72 <param name="settings" value="" />
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73 <output name="output" file="histogramdiscrete.000.txt" lines_diff="2"/>
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74 </test>
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75 <test>
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76 <param name="input" value="tabular_matrix.txt" />
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77 <param name="module" value="heatmap" />
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78 <param name="columns" value="key1: 1, key2: 2, key3: 3" />
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79 <param name="settings" value="" />
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80 <output name="output" file="heatmap.000.txt" lines_diff="2"/>
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81 </test>
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20
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82 </tests>
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83 </tool> |
