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6
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1 <tool id="getDistribution" name="get distribution">
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15
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2 <description>Get Distribution: Get the distribution of the genomic coordinates along a genome.</description>
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6
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3 <command interpreter="python">
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4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #elif $formatType.FormatInputFileName == 'csv':
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14 -f csv
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15 #elif $formatType.FormatInputFileName == 'sam':
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16 -f sam
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17 #elif $formatType.FormatInputFileName == 'gtf':
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18 -f gtf
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19 #end if
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20
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21 -r $refFile
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22
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23 #if $optionNbBin.Nb == 'Yes':
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24 -b $optionNbBin.nbBins
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25 #end if
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26
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27 #if $optionStart.start == 'Yes':
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28 -s $optionStart.startValue
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29 #end if
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30
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31 #if $optionEnd.end == 'Yes':
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32 -e $optionEnd.endValue
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33 #end if
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34
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35 #if $optionHeight.height == 'Yes':
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36 -H $optionHeight.heightValue
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37 #end if
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38
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39 #if $optionWidth.width == 'Yes':
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40 -W $optionWidth.widthValue
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41 #end if
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42
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43 #if $optionYMin.YMin == 'Yes':
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44 -y $optionYMin.YMinValue
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45 #end if
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46
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47 #if $optionYMax.YMax == 'Yes':
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48 -Y $optionYMax.YMaxValue
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49 #end if
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50
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51 #if $optionChrom.chrom == 'Yes':
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52 -c $optionChrom.chromValue
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53 #end if
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54
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55 #if $optionColor.color == 'Yes':
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56 -l $optionColor.colorValue
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57 #end if
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58
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59 $bothStrands
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60 $average
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61 $normalize
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62 $csv $outputCSV
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63 $gff $outputGFF
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64 -m
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65 -o $outputFile
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66
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67 </command>
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68
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69 <inputs>
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70 <conditional name="formatType">
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71 <param name="FormatInputFileName" type="select" label="Input File Format">
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72 <option value="bed">bed</option>
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73 <option value="gff">gff</option>
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74 <option value="gff2">gff2</option>
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75 <option value="gff3">gff3</option>
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76 <option value="sam">sam</option>
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77 <option value="gtf">gtf</option>
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78 </param>
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79 <when value="bed">
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80 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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81 </when>
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82 <when value="gff">
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83 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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84 </when>
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85 <when value="gff2">
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86 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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87 </when>
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88 <when value="gff3">
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89 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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90 </when>
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91 <when value="sam">
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92 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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93 </when>
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94 <when value="gtf">
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95 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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96 </when>
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97 </conditional>
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98
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99 <param name="refFile" format="fasta" type="data" label="reference genome file"/>
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100
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101 <conditional name="optionNbBin">
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102 <param name="Nb" type="select" label="number of points">
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103 <option value="Yes">Yes</option>
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104 <option value="No" selected="true">No</option>
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105 </param>
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106 <when value="Yes">
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107 <param name="nbBins" type="integer" value="1000" />
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108 </when>
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109 <when value="No">
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110 </when>
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111 </conditional>
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112
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113 <conditional name="optionChrom">
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114 <param name="chrom" type="select" label="if you wish to plot only one chromosome, mention the chromosome name">
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115 <option value="Yes">Yes</option>
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116 <option value="No" selected="true">No</option>
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117 </param>
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118 <when value="Yes">
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119 <param name="chromValue" type="text" value="chromName" />
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120 </when>
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121 <when value="No">
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122 </when>
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123 </conditional>
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124
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125 <conditional name="optionStart">
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126 <param name="start" type="select" label="if you wish to plot only one locus, mention its start position">
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127 <option value="Yes">Yes</option>
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128 <option value="No" selected="true">No</option>
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129 </param>
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130 <when value="Yes">
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131 <param name="startValue" type="integer" value="0" />
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132 </when>
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133 <when value="No">
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134 </when>
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135 </conditional>
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136
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137 <conditional name="optionEnd">
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138 <param name="end" type="select" label="if you wish to plot only one locus, mention its end position">
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139 <option value="Yes">Yes</option>
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140 <option value="No" selected="true">No</option>
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141 </param>
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142 <when value="Yes">
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143 <param name="endValue" type="integer" value="0" />
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144 </when>
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145 <when value="No">
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146 </when>
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147 </conditional>
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148
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149 <conditional name="optionHeight">
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150 <param name="height" type="select" label="height of the figure">
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151 <option value="Yes">Yes</option>
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152 <option value="No" selected="true">No</option>
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153 </param>
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154 <when value="Yes">
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155 <param name="heightValue" type="integer" value="300" />
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156 </when>
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157 <when value="No">
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158 </when>
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159 </conditional>
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160
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161 <conditional name="optionWidth">
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162 <param name="width" type="select" label="width of the figure">
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163 <option value="Yes">Yes</option>
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164 <option value="No" selected="true">No</option>
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165 </param>
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166 <when value="Yes">
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167 <param name="widthValue" type="integer" value="1000" />
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168 </when>
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169 <when value="No">
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170 </when>
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171 </conditional>
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172
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173 <conditional name="optionYMin">
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174 <param name="YMin" type="select" label="minimum value on the y-axis to plot">
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175 <option value="Yes">Yes</option>
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176 <option value="No" selected="true">No</option>
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177 </param>
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178 <when value="Yes">
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179 <param name="YMinValue" type="integer" value="1000" />
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180 </when>
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181 <when value="No">
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182 </when>
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183 </conditional>
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184
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185 <conditional name="optionYMax">
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186 <param name="YMax" type="select" label="maximum value on the y-axis to plot">
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187 <option value="Yes">Yes</option>
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188 <option value="No" selected="true">No</option>
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189 </param>
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190 <when value="Yes">
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191 <param name="YMaxValue" type="integer" value="1000" />
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192 </when>
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193 <when value="No">
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194 </when>
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195 </conditional>
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196
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197 <conditional name="optionColor">
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198 <param name="color" type="select" label="color of the lines (separated by commas and no space)">
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199 <option value="Yes">Yes</option>
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200 <option value="No" selected="true">No</option>
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201 </param>
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202 <when value="Yes">
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203 <param name="colorValue" type="text" value="red,blue" />
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204 </when>
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205 <when value="No">
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206 </when>
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207 </conditional>
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208
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209 <param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/>
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210 <param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot the number of element per bin (instead of sum)"/>
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211
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212 <conditional name="optionNames">
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213 <param name="names" type="select" label="name for the tags (separated by commas and no space)">
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214 <option value="Yes">Yes</option>
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215 <option value="No" selected="true">No</option>
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216 </param>
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217 <when value="Yes">
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218 <param name="namesValue" type="text" value="nbElements" />
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219 </when>
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220 <when value="No">
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221 </when>
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222 </conditional>
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223
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224 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panel sizes are different)"/>
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225 </inputs>
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226
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227 <outputs>
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228 <data name="outputFile" format="png" label="[getDistribution] out png file"/>
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229 </outputs>
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230
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231 <help>
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232 This script gives a .tar out file, if you want to take look at the results, you have to download it.
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233
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234 Print a density profile of the data for each chromosome, see Figure~\ref{fig:getDistribution}. You have to provide the reference genome, to know the sizes of the chromosomes. You can also provide the number of points (called *bins*) you want per chromosome.
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235
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236 By default, only one curve is plotted per chromosome, but you can plot one curve per strand and per chromosome (the minus strand will be plotted with non-positive values on the *y*-axis).
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237
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238 If you want, you can also plot a specific region, by mentionning the chromosome, the start and the end positions of the region.
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239 </help>
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240 </tool>
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