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83
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1 <macros>
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2 <token name="@VERSION@">1.0.0</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement>
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6 </requirements>
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7 </xml>
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8
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9 <xml name="alignment-s">
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10 <conditional name="conditionalscale">
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11 <param name="alignment" type="select" label="Region alignment" help="">
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12 <option value="center">Center - Alignment on the central position</option>
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13 <option value="left">Left - Alignment on the starting position</option>
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14 <option value="right">Right - Alignment on the ending position</option>
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15 <option value="scale">Scale - Scaling all regions to the same length</option>
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16 </param>
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17 <when value="center">
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18 <!-- fill gaps -->
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19 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
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20 </when>
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21 <when value="left">
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22 <!-- fill gaps -->
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23 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
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24 </when>
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25 <when value="right">
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26 <!-- fill gaps -->
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27 <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
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28 </when>
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29 <when value="scale">
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30 <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
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31 </when>
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32 </conditional>
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33 </xml>
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34
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35 <xml name="alignment">
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36 <param name="alignment" type="select" label="Region alignment" help="">
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37 <option value="center">Center - Alignment on the central position</option>
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38 <option value="left">Left - Alignment on the starting position</option>
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39 <option value="right">Right - Alignment on the ending position</option>
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40 </param>
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41 </xml>
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42
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43 <xml name="citations">
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44 <citations>
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45 <citation type="doi">10.1080/10485252.2017.1306627</citation>
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89
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46 <citation type="doi">10.1093/bioinformatics/bty090</citation>
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83
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47 </citations>
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48 </xml>
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49
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50 <xml name="plot-params">
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51 <!-- average -->
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52 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
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53 <!-- average -->
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54 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
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55 <!-- conditional plot type -->
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56 <conditional name="conditionalplottype">
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57 <!-- plot type -->
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58 <param name="plottype" type="select" label="Plot type">
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59 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
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60 <option value="curves">Curves (aligned)</option>
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61 </param>
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62 <!-- conditional choice: plottype=boxplot -->
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63 <when value="boxplot">
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64 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
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65 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
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66 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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67 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
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68 <repeat name="probabilities" title="Probabilities">
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69 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
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70 </repeat>
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71 </section>
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72 </when>
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73 </conditional>
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74 </xml>
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75
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76 <xml name="plot-sum">
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77 <section name="plotsum" title="Summary plot" expanded="True">
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78 <!-- conditional group by -->
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79 <conditional name="conditionalgroupby">
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80 <!-- group by -->
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81 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
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82 <option value="none">No plot</option>
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83 <option value="test">Group by test</option>
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84 <option value="feature">Group by feature</option>
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85 </param>
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86 <when value="test">
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87 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
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88 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
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89 </when>
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90 <when value="feature">
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91 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
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92 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
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93 </when>
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94 </conditional>
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95 </section>
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96 </xml>
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97 </macros> |
