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31
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1 <tool id="CompareOverlapping" name="Compare Overlapping">
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6
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2 <description>Print all the transcripts from a first file which overlap with the transcripts from a second file.</description>
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3 <command interpreter="python">
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4 ../Java/Python/CompareOverlapping.py -i $formatType.inputFileName1
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5 #if $formatType.FormatInputFileName1 == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName1 == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName1 == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName1 == 'gff3':
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12 -f gff3
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13 #elif $formatType.FormatInputFileName1 == 'sam':
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14 -f sam
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15 #elif $formatType.FormatInputFileName1 == 'gtf':
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16 -f gtf
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17 #end if
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18
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19 -j $formatType2.inputFileName2
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20 #if $formatType2.FormatInputFileName2 == 'bed':
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21 -g bed
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22 #elif $formatType2.FormatInputFileName2 == 'gff':
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23 -g gff
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24 #elif $formatType2.FormatInputFileName2 == 'gff2':
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25 -g gff2
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26 #elif $formatType2.FormatInputFileName2 == 'gff3':
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27 -g gff3
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28 #elif $formatType2.FormatInputFileName2 == 'sam':
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29 -g sam
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30 #elif $formatType2.FormatInputFileName2 == 'gtf':
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31 -g gtf
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32 #end if
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33
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34 -o $outputFileGff
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35
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36 #if $optionNFirstFile1.NFirstForFile1 == 'Yes':
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37 -S $optionNFirstFile1.firstNtFile1
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38 #end if
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39 #if $optionNFirstFile2.NFirstForFile2 == 'Yes':
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40 -s $optionNFirstFile2.firstNtFile2
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41 #end if
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42 #if $optionNLastFile1.NLastForFile1 == 'Yes':
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43 -U $optionNLastFile1.lastNtFile1
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44 #end if
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45 #if $optionNLastFile2.NLastForFile2 == 'Yes':
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46 -u $optionNLastFile2.lastNtFile2
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47 #end if
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48
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49 #if $optionExtentionCinqFile1.extentionFile1 == 'Yes':
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50 -E $optionExtentionCinqFile1.extention51
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51 #end if
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52 #if $optionExtentionCinqFile2.extentionFile2 == 'Yes':
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53 -e $optionExtentionCinqFile2.extention52
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54 #end if
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55
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56 #if $optionExtentionTroisFile1.extentionFile1 == 'Yes':
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57 -N $optionExtentionTroisFile1.extention31
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58 #end if
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59 #if $optionExtentionTroisFile2.extentionFile2 == 'Yes':
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60 -n $optionExtentionTroisFile2.extention32
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61 #end if
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62
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63 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
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64 -c
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65 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
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66 -a
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67 #end if
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68
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69 #if $OptionDistance.Dist == 'Yes':
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70 -d $OptionDistance.distance
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71 #end if
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72
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73 #if $OptionMinOverlap.MO == 'Yes':
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74 -m $OptionMinOverlap.minOverlap
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75 #end if
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76
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77 $InvertMatch
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78 $ReportIntron
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79 $NotOverlapping
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80
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81 </command>
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82
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83 <inputs>
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84 <conditional name="formatType">
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85 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
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86 <option value="bed">bed</option>
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87 <option value="gff">gff</option>
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88 <option value="gff2">gff2</option>
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89 <option value="gff3">gff3</option>
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90 <option value="sam">sam</option>
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91 <option value="gtf">gtf</option>
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92 </param>
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93 <when value="bed">
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94 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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95 </when>
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96 <when value="gff">
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97 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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98 </when>
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99 <when value="gff2">
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100 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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101 </when>
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102 <when value="gff3">
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103 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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104 </when>
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105 <when value="sam">
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106 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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107 </when>
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108 <when value="gtf">
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109 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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31
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110 </when>
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6
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111 </conditional>
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112
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113 <conditional name="formatType2">
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114 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
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115 <option value="bed">bed</option>
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116 <option value="gff">gff</option>
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117 <option value="gff2">gff2</option>
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118 <option value="gff3">gff3</option>
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119 <option value="sam">sam</option>
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120 <option value="gtf">gtf</option>
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121 </param>
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122 <when value="bed">
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123 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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124 </when>
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125 <when value="gff">
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126 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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127 </when>
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128 <when value="gff2">
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129 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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130 </when>
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131 <when value="gff3">
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132 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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133 </when>
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134 <when value="sam">
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135 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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136 </when>
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137 <when value="gtf">
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138 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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139 </when>
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140 </conditional>
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141
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31
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142
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143
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144 <conditional name="optionNFirstFile1">
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31
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145 <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">
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6
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146 <option value="Yes">Yes</option>
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147 <option value="No" selected="true">No</option>
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148 </param>
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149 <when value="Yes">
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31
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150 <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />
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6
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151 </when>
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152 <when value="No">
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153 </when>
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154 </conditional>
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155 <conditional name="optionNFirstFile2">
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31
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156 <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2">
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6
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157 <option value="Yes">Yes</option>
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158 <option value="No" selected="true">No</option>
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159 </param>
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160 <when value="Yes">
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31
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161 <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" />
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6
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162 </when>
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163 <when value="No">
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164 </when>
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165 </conditional>
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166
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167 <conditional name="optionNLastFile1">
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31
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168 <param name="NLastForFile1" type="select" label="NLast for file 1">
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169 <option value="Yes">Yes</option>
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170 <option value="No" selected="true">No</option>
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171 </param>
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172 <when value="Yes">
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31
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173 <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/>
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6
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174 </when>
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175 <when value="No">
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176 </when>
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177 </conditional>
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178 <conditional name="optionNLastFile2">
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31
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179 <param name="NLastForFile2" type="select" label="NLast for file 2">
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6
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180 <option value="Yes">Yes</option>
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181 <option value="No" selected="true">No</option>
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182 </param>
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183 <when value="Yes">
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31
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184 <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>
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6
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185 </when>
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186 <when value="No">
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187 </when>
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188 </conditional>
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189
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31
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190
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191
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6
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192 <conditional name="optionExtentionCinqFile1">
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31
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193 <param name="extentionFile1" type="select" label="Extension towards 5 for file 1">
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194 <option value="Yes">Yes</option>
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195 <option value="No" selected="true">No</option>
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196 </param>
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197 <when value="Yes">
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198 <param name="extention51" type="integer" value="1" label="in file 1" />
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199 </when>
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200 <when value="No">
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201 </when>
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202 </conditional>
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203
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31
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204
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205 <conditional name="optionExtentionCinqFile2">
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31
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206 <param name="extentionFile2" type="select" label="Extension towards 5 for file 2">
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207 <option value="Yes">Yes</option>
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208 <option value="No" selected="true">No</option>
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209 </param>
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210 <when value="Yes">
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211 <param name="extention52" type="integer" value="1" label="in file 2"/>
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212 </when>
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213 <when value="No">
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214 </when>
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215 </conditional>
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216
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217 <conditional name="optionExtentionTroisFile1">
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31
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218 <param name="extentionFile1" type="select" label="Extension towards 3 for file 1">
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219 <option value="Yes">Yes</option>
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220 <option value="No" selected="true">No</option>
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221 </param>
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222 <when value="Yes">
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223 <param name="extention31" type="integer" value="1" label="in file 1" />
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224 </when>
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225 <when value="No">
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226 </when>
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227 </conditional>
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228
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229 <conditional name="optionExtentionTroisFile2">
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31
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230 <param name="extentionFile2" type="select" label="Extension towards 3 for file 2">
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231 <option value="Yes">Yes</option>
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232 <option value="No" selected="true">No</option>
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233 </param>
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234 <when value="Yes">
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235 <param name="extention32" type="integer" value="1" label="in file 2" />
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236 </when>
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237 <when value="No">
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238 </when>
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239 </conditional>
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240
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241 <conditional name="OptionColinearOrAntiSens">
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31
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242 <param name="OptionCA" type="select" label="Colinear or anti-sens">
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6
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243 <option value="Colinear">Colinear</option>
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244 <option value="AntiSens">AntiSens</option>
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245 <option value="NONE" selected="true">NONE</option>
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246 </param>
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247 <when value="Colinear">
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248 </when>
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249 <when value="AntiSens">
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250 </when>
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251 <when value="NONE">
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252 </when>
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253 </conditional>
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254
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255 <conditional name="OptionDistance">
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256 <param name="Dist" type="select" label="Maximum Distance between two reads">
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257 <option value="Yes">Yes</option>
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258 <option value="No" selected="true">No</option>
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259 </param>
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260 <when value="Yes">
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261 <param name="distance" type="integer" value="0"/>
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262 </when>
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263 <when value="No">
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264 </when>
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265 </conditional>
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266
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267 <conditional name="OptionMinOverlap">
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268 <param name="MO" type="select" label="Minimum number of overlapping between two reads">
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269 <option value="Yes">Yes</option>
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270 <option value="No" selected="true">No</option>
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271 </param>
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272 <when value="Yes">
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273 <param name="minOverlap" type="integer" value="1"/>
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274 </when>
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275 <when value="No">
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276 </when>
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277 </conditional>
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31
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278 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
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279 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>
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280 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
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281
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282 </inputs>
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283
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6
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284 <outputs>
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285 <data name="outputFileGff" format="gff3"/>
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286 </outputs>
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287
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288 </tool>
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