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1 <tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
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2 <description>on Test Scale</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <!--<expand macro="requirements" />-->
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7
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
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11 iwtomicsrdata='${rdata}'
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12 iwtomicstests='${testids}'
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13 iwtomicsselectedfeatures='${featureids}'
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14
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15 #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
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16 test_subset='${test_subset}'
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17 #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
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18 feature_subset='${feature_subset}'
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19 #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
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20 scale_subset='c(${scale_subset})'
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21
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22 testalpha='${plotres.alpha}'
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23 average='${plotres.average}'
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24 size='${plotres.size}'
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25 plottype="'${plotres.conditionalplottype.plottype}'"
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26 #if $plotres.conditionalplottype.plottype == 'boxplot':
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27 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
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28 #if $probs != "":
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29 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
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30 #else:
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31 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
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32 #end if
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33 #end if
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34
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35 groupby="'${plotsum.conditionalgroupby.groupby}'"
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36 #if $plotsum.conditionalgroupby.groupby == "test":
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37 summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
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38 only_significant='${plotsum.conditionalgroupby.testonlysig}'
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39 #elif $plotsum.conditionalgroupby.groupby == "feature":
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40 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
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41 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
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42 #end if
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43 ]]>
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44 </command>
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45
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46 <inputs>
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47 <!-- RData -->
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48 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
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49 <!-- test IDs -->
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50 <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
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51 <!-- feature IDs -->
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52 <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
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53
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54 <!-- repeat threshold on test scale -->
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55 <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
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56 <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
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57 <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
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58 <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
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59 <param name="scale" type="integer" value="0" min="0" label="Scale" />
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60 </repeat>
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61 </section>
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62
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63 <!-- plot IWTomics results -->
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64 <section name="plotres" title="Plot IWTomics test results" expanded="True">
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65 <!-- alpha -->
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66 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
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67 <expand macro="plot-params" />
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68 </section>
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69
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70 <!-- summary plot -->
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71 <expand macro="plot-sum" />
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72 </inputs>
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73
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74 <outputs>
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75 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
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76 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
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77 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
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78 </outputs>
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79
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80 <tests>
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81 <test>
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82 <param name="rdata" value="output_testandplot/iwtomics.testandplot.RData" ftype="rdata" />
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83 <param name="testids" value="output_testandplot/iwtomics.testandplot.tests.txt" ftype="tabular" />
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84 <param name="featureids" value="output_testandplot/iwtomics.testandplot.selectedfeatures.txt" ftype="tabular" />
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85 <repeat name="thresholdontestscale">
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86 <param name="test" value="1" />
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87 <param name="feature" value="1" />
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88 <param name="scale" value="10" />
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89 </repeat>
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90 <repeat name="thresholdontestscale">
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91 <param name="test" value="1,2,3" />
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92 <param name="feature" value="2" />
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93 <param name="scale" value="20" />
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94 </repeat>
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95 <param name="alpha" value="0.05" />
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96 <param name="average" value="TRUE" />
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97 <param name="size" value="TRUE" />
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98 <param name="plottype" value="boxplot" />
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99 <param name="prob0" value="0.25" />
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100 <param name="prob1" value="0.5" />
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101 <param name="prob2" value="0.75" />
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102 <param name="groupby" value="feature" />
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103 <param name="featurealphaplot" value="0.05" />
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104 <param name="featureonlysig" value="TRUE" />
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105 <output name="adjustedpvalue" file="output_plotwithscale/iwtomics.plotwithscale.adjustedpvalue.txt" compare="sim_size" />
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106 <output name="iwtomicsrespdf" file="output_plotwithscale/iwtomics.plotwithscale.iwtomicstestresults.pdf" compare="sim_size" />
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107 <output name="iwtomicssumpdf" file="output_plotwithscale/iwtomics.plotwithscale.summaryplot.pdf" compare="sim_size" />
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108 </test>
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109 </tests>
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110
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111 <help><![CDATA[
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112 This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
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113 for the different tests performed at the selected scale, and it creates a graphical representation of the
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114 Interval-Wise Testing results and a summary plot (optional) at the selected scale.
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115
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116 -----
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117
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118 **Input files**
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119
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120 RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
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121 These files are created by the tool *IWTomics Test and Plot*.
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122
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123 -----
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124
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125 **Output**
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126
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127 The tool returns:
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128
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129 1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
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130 2. PDF file with the plotted test results;
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131 3. PDF file with the summary plot.
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132
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133 -----
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134
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135 .. class:: infomark
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136
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137 **Notes**
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138
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139 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
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140
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141 It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
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142 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
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143
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144 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
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145 ]]></help>
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146
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147 <expand macro="citations" />
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148
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149 </tool>
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