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1 <tool id="iwtomics_loadandplot" name="IWTomics Load" version="@VERSION@.0">
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2 <description>Smooth and Plot</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 '$__tool_directory__/loadandplot.R' outrdata='${outrdata}' outregions='${outregions}' outfeatures='${outfeatures}' outpdf='${outpdf}'
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11
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12 #set region_paths = '|'.join( [ str( $r ) for $r in $regions ] )
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13 regionspaths='${region_paths}'
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14 #set region_galaxyids = ','.join( [ str( $r.hid ) for $r in $regions ] )
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15 regionsgalaxyids='c(${region_galaxyids})'
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16 #set region_names = '|'.join( [ str( $r.name ) for $r in $regions ] )
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17 regionsfilenames='${region_names}'
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85
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18 #if $regionsheader:
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19 regionsheaderfile='${region_header}'
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20 #end if
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21
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22 #set feature_paths = '|'.join( [ str( $f ) for $f in $features ] )
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23 featurespaths='${feature_paths}'
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24 #set feature_galaxyids = ','.join( [ str( $f.hid ) for $f in $features ] )
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25 featuresgalaxyids='c(${feature_galaxyids})'
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26 #set feature_names = '|'.join( [ str( $f.name ) for $f in $features ] )
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27 featuresfilenames='${feature_names}'
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85
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28 #if $featuresheader:
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83
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29 featuresheaderfile='${feature_header}'
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30 #end if
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31
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32 smoothing="'${conditionaltype.smoothing}'"
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33 start.are.0based='${zerobased}'
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34 #if $conditionaltype.smoothing == 'no':
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35 alignment="'${conditionaltype.alignment}'"
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36 #elif $conditionaltype.smoothing == 'locpoly':
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37 bandwidth='${conditionaltype.locpolybandwidth}'
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38 degree='${conditionaltype.locpolydegree}'
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39 alignment="'${conditionaltype.conditionalscale.alignment}'"
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40 #elif $conditionaltype.smoothing == 'kernel':
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41 bandwidth='${conditionaltype.kernelbandwidth}'
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42 alignment="'${conditionaltype.conditionalscale.alignment}'"
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43 #elif $conditionaltype.smoothing == 'splines':
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44 degree='${conditionaltype.splinesdegree}'
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45 dist_knots='${conditionaltype.splinesdistknots}'
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46 alignment="'${conditionaltype.conditionalscale.alignment}'"
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47 #end if
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48
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49 #if $conditionaltype.smoothing != 'no':
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50 #if $conditionaltype.conditionalscale.alignment == 'scale':
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51 scale='${conditionaltype.conditionalscale.scalegrid}'
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52 fill_gaps='TRUE'
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53 #else
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54 fill_gaps='${conditionaltype.conditionalscale.fillgaps}'
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55 #end if
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56 #end if
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57
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58 average='${plotres.average}'
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59 size='${plotres.size}'
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60 plottype="'${plotres.conditionalplottype.plottype}'"
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61 #if $plotres.conditionalplottype.plottype == 'boxplot':
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62 #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
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63 #if $probs != "":
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64 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
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65 #else:
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66 probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
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67 #end if
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68 #end if
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69 ]]>
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70 </command>
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71
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72 <inputs>
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73 <!-- regions -->
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74 <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
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75 <param format="tabular" name="regionsheader" type="data" label="Insert header file for regions (optional)" optional="true" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output." />
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76
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77 <!-- features -->
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78 <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
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79 <param format="tabular" name="featuresheader" type="data" label="Insert header file for features (optional)" optional="true" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output." />
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80
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81 <!-- zero-base one-base -->
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82 <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
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83 <option value="TRUE">0-based</option>
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84 <option value="FALSE">1-based</option>
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85 </param>
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86
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87 <!-- conditional smoothing -->
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88 <conditional name="conditionaltype">
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89 <!-- smoothing -->
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90 <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
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91 <option value="no">No</option>
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92 <option value="locpoly">Local Polynomials</option>
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93 <option value="kernel">Gaussian Kernel</option>
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94 <option value="splines">B-Splines</option>
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95 </param>
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96 <!-- conditional choice: smoothing=no -->
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97 <when value="no">
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98 <expand macro="alignment" />
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99 </when>
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100 <!-- conditional choice: smoothing=locpoly -->
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101 <when value="locpoly">
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102 <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
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103 <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
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104 <!-- conditional region alignment -->
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105 <expand macro="alignment-s" />
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106 </when>
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107 <!-- conditional choice: smoothing=kernel -->
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108 <when value="kernel">
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109 <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
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110 <!-- conditional region alignment -->
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111 <expand macro="alignment-s" />
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112 </when>
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113 <!-- conditional choice: smoothing=splines -->
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114 <when value="splines">
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115 <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
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116 <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
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117 <!-- conditional region alignment -->
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118 <expand macro="alignment-s" />
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119 </when>
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120 </conditional>
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121
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122 <!-- plot IWTomics results -->
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123 <section name="plotres" title="Plot data" expanded="True">
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124 <expand macro="plot-params" />
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125 </section>
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126 </inputs>
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127
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128 <outputs>
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129 <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
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130 <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
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131 <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
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132 <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
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133 </outputs>
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134
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135 <tests>
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136 <test>
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137 <param name="regions" value="input/Controls_regions.bed,input/Elements1_regions.bed,input/Elements2_regions.bed,input/Elements3_regions.bed" ftype="bed" />
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138 <param name="regionsheader" value="input/regions.header.txt" ftype="tabular" />
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139 <param name="features" value="input/Feature1.bed,input/Feature2.bed" ftype="bed" />
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140 <param name="featuresheader" value="input/features.header.bed.txt" ftype="tabular" />
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141 <param name="zerobased" value="TRUE" />
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142 <param name="smoothing" value="kernel" />
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143 <param name="alignment" value="center" />
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144 <param name="kernelbandwidth" value="5" />
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145 <param name="fillgaps" value="TRUE" />
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146 <param name="average" value="TRUE" />
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147 <param name="size" value="TRUE" />
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148 <param name="plottype" value="boxplot" />
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149 <param name="prob0" value="0.25" />
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150 <param name="prob1" value="0.5" />
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151 <param name="prob2" value="0.75" />
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152 <output name="outrdata" file="output_loadandplot/iwtomics.loadandplot.RData" compare="sim_size" />
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153 <output name="outregions" file="output_loadandplot/iwtomics.loadandplot.regions.txt" />
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154 <output name="outfeatures" file="output_loadandplot/iwtomics.loadandplot.features.txt" />
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155 <output name="outpdf" file="output_loadandplot/iwtomics.loadandplot.pdf" compare="sim_size" />
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156 </test>
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157 </tests>
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158
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159 <help><![CDATA[
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160 This tool imports a collection of genomic region datasets, and associates to each region
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161 multiple genomic feature measurements. It allows to align the regions in multiple ways
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162 (center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
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163 measurements) and to create a graphical representation of the feature measurements in each
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164 region datasets (aligned curves or pointwise quantile curves).
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165
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166 -----
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167
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168 **Region datasets**
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169
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170 Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
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171 start end (extra columns present in the input file are ignored). Regions can be of different
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172 length::
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173
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174 chr2 49960150 50060150
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175 chr2 55912445 56012445
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176 ...
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177
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178 -----
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179
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180 **Feature measurements**
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181
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182 Feature measurements corresponding to all the regions can be provided as a BED or Tabular
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183 file with tab delimited columns chr start end value::
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184
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185 chr2 49960150 49962150 0.9426
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186 chr2 49962150 49964150 0.7816
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187 ...
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188
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189 Each feature must be measured in windows of a fixed size inside all the regions (missing
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190 values must be indicated as NA). Another way to import feature measurements is from a
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191 Tabular file with the first three columns chr start end corresponding to the different genomic
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192 regions, followed on the same row by all the measurements in fixed-size windows::
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193
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194 chr2 49960150 50060150 0.9426 0.7816 0.8921 ... ... 1.2063
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195 chr2 55912445 56012445 0.8719 0.9975 1.1619 ... ... 0.9601
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196 ...
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197
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198 -----
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199
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200 **Output**
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201
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202 The tool returns:
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203
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204 1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
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205 2. Region dataset identifiers;
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206 3. Feature identifiers;
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207 4. PDF file with the plotted data.
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208
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209 1-3 can be used as input of the tool *IWTomics Test and Plot*
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210
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211 -----
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212
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213 .. class:: infomark
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214
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215 **Notes**
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216
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217 This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy - fabio.cumbo@iasi.cnr.it) and Marzia A. Cremona (The Pennsylvania State University, USA - mac78@psu.edu).
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218
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219 It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
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220 The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
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221
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222 .. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
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223
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224 Example data can be found at:
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225
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226 1. Simulated_data_
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227 2. ETn_data_
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228
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229 .. _Simulated_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-example
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230 .. _ETn_data: https://usegalaxy.org/u/fabio-cumbo/h/iwtomics-etn-example
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231 ]]></help>
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232
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233 <expand macro="citations" />
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234
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235 </tool>
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