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1 <tool id="karyotype_Plot_1" name="Karyotype Plotting tool" version="1.0.0">
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2 <description>for multiple series </description>
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3
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3 <command interpreter="bash">r_wrapper.sh $script_file</command>
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4
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5 <inputs>
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6 <param name="main" type="text" value="" size="30" label="Plot Title"/>
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7 <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
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8 <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
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9 <param name="lty" type="select" label="Backbone Line Type">
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10 <option value="1">Solid</option>
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11 <option value="2">Dashed</option>
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12 <option value="3">Dotted</option>
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13 </param>
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14 <param name="col" type="select" label="Backbone Line Color">
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15 <option value="1">Black</option>
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16 <option value="2">Red</option>
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17 <option value="3">Green</option>
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18 <option value="4">Blue</option>
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19 <option value="5">Cyan</option>
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20 <option value="6">Magenta</option>
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21 <option value="7">Yellow</option>
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22 <option value="8">Gray</option>
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23 </param>
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24 <param name="lwd" type="float" label="Backbone Line Width" value="1.0"/>
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25
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26 <conditional name="legend">
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27 <param name="status" type="select" label="Include legend?">
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28 <option value="yes" selected="true">Yes</option>
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29 <option value="no">No</option>
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30 </param>
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31 <when value="yes">
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32 <param name="leg_title" type="text" value="" size="30" label="Legend title"/>
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33 <param name="leg_pos" type="select" label="Legend position">
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34 <option value="top" selected="true">top</option>
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35 <option value="topright">topright</option>
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36 <option value="topleft">topleft</option>
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37 <option value="bottom">bottom</option>
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38 <option value="bottomright">bottomright</option>
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39 <option value="bottomleft">bottomleft</option>
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40 <option value="left">left</option>
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41 <option value="right">right</option>
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42 <option value="center">center</option>
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43 </param>
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44 </when>
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45 <when value="no">
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46 </when>
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47 </conditional>
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48
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49 <repeat name="series" title="Series">
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50 <param name="input" type="data" format="tabular" label="Dataset"/>
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51 <param name="chrcolumn" type="data_column" data_ref="input" label="Chromosome Column"/>
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52 <param name="startcolumn" type="data_column" data_ref="input" numerical="True" label="Start Column"/>
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53 <param name="endcolumn" type="data_column" data_ref="input" numerical="True" label="End Column"/>
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54 <param name="fpch" type="select" label="Point Type">
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55 <option value="1">Circle (hollow)</option>
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56 <option value="2">Triangle (hollow)</option>
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57 <option value="3">Cross</option>
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58 <option value="4">Diamond (hollow)</option>
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59 <option value="15">Square (filled)</option>
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60 <option value="16">Circle (filled)</option>
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61 <option value="17">Triangle (filled)</option>
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62 </param>
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63 <param name="fcol" type="select" label="Point Color">
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64 <option value="1">Black</option>
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65 <option value="2">Red</option>
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66 <option value="3">Green</option>
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67 <option value="4">Blue</option>
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68 <option value="5">Cyan</option>
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69 <option value="6">Magenta</option>
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70 <option value="7">Yellow</option>
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71 <option value="8">Gray</option>
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72 </param>
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73 <param name="fcex" type="float" label="Point Scale" value="1.0"/>
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74 <param name="leg_text" type="text" value="" size="30" label="Legend text" help="Will be printed only if Include Legend option is set to Yes"/>
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75 </repeat>
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76 </inputs>
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77
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78 <configfiles>
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79 <configfile name="script_file">
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80 ## Setup R error handling to go to stderr
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81 options( show.error.messages=F,
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82 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) },
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83 warn = -1 )
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84 ## Determine range of all series in the plot
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85 library('gtools')
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86 chrlist = c()
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87 coordrange = c( NULL, NULL )
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88 #for $i, $s in enumerate( $series )
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89 s${i} = read.table( "${s.input.file_name}" )
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90 chrlist = union( chrlist, as.character(unique(s${i}[,${s.chrcolumn}])) )
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91 coordrange = range( coordrange, range(s${i}[,${s.startcolumn}]), range(s${i}[,${s.endcolumn}]) )
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92 #end for
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93 chrlist=mixedsort(chrlist)
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94 coordrange_byChr=list()
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95 length(coordrange_byChr) = length(chrlist)*2
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96 dim(coordrange_byChr) = c(length(chrlist),2)
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97 ci=1
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98 for (chr in chrlist) {
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99 #for $i, $s in enumerate( $series )
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100 s${i} = read.table( "${s.input.file_name}" )
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101 if (nrow(s${i}[s${i}[,${s.chrcolumn}]==chr,]) > 0) {
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102 coordrange_byChr[ci,]=range(coordrange_byChr[ci,], s${i}[s${i}[,${s.chrcolumn}]==chr,c(${s.startcolumn},${s.endcolumn})])
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103 }
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104 #end for
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105 ci=ci+1
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106 }
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107 ## Open output PDF file
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108 pdf( "${out_file1}" )
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109 ## Dummy plot for axis / labels
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110 plot( NULL, type="n", xlim=c(1,length(chrlist)), ylim=coordrange, axes=F, main="${main}", xlab="${xlab}", ylab="${ylab}" )
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111 box()
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112 axis(1,at=1:length(chrlist),labels=chrlist,cex.axis=0.9, las=2)
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113 axis(2,at=seq(coordrange[1],coordrange[2], length.out=10))
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114 ## Plot backbone lines for each chr
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115 ci=1
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116 for (chr in chrlist) {
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117 lines(c(ci,ci),coordrange_byChr[ci,],lty=${lty},col=${col},lwd=${lwd})
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118 ci=ci+1
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119 }
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120
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121 legend_text=c()
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122 pchlist=c()
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123 colorlist=c()
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124 ## Plot each series
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125 #for $i, $s in enumerate( $series )
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126 chrs=as.character(s${i}[,${s.chrcolumn}])
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127 xvals=sapply(chrs,function(x) which(chrlist==x))
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128 points(xvals, s${i}[,${s.startcolumn}], pch=${s.fpch}, cex=${s.fcex}, col=${s.fcol} )
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129 legend_text[${i}+1] = "${s.leg_text}"
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130 pchlist[${i}+1] = ${s.fpch}
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131 colorlist[${i}+1] = ${s.fcol}
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132 #end for
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133
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134 #if $legend['status'] == "yes"
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135 legend_title = "$legend.leg_title"
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136 legend_pos = "$legend.leg_pos"
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137 legend(legend_pos, title=legend_title, legend=legend_text, pch=pchlist, col=colorlist)
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138 #end if
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139
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140 ## Close the PDF file
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141 devname = dev.off()
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142 </configfile>
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143 </configfiles>
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144
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145 <outputs>
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146 <data format="pdf" name="out_file1" />
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147 </outputs>
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148
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149 <requirements>
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150 <requirement type="set_environment">R_SCRIPT_PATH</requirement>
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151 <requirement type="package" version="2.15.0">R</requirement>
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152 </requirements>
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153
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154 <help>
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155 .. class:: infomark
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156
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157 **What it does**
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158
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159 This tool allows you to paint genomic regions of interest on chromosomes arranged in a karyotype-like fashion. It also allows you to have multiple series in a plot, with each series corresponding to a different feature/dataset.
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160
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161 -----
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162
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163 .. class:: warningmark
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164
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165 Chromosome lengths (backbone line) are determined based on min and max co-ordinates (by chromosome) in start and end columns respectively. For the series, only the co-ordiantes in start column are used for plotting.
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166
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167 -----
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168
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169 **Example**
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170
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171 Below is an example of a two series karyotype plot:
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172
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173 .. image:: ./static/operation_icons/karyotype_output.png
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174 :height: 540
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175 :width: 540
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176
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177 </help>
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178 </tool>
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