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1 <tool id="ComputeCoverage" name="compute coverage">
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2 <description>Compute the coverage of a set with respect to another set.</description>
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3 <command interpreter="python">
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4 ../Java/Python/ComputeCoverage.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 $ReportIntron
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35 -o $outputFileGff
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36
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37 </command>
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38
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39 <inputs>
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40 <conditional name="formatType">
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41 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
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42 <option value="bed">bed</option>
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43 <option value="gff">gff</option>
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44 <option value="gff2">gff2</option>
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45 <option value="gff3">gff3</option>
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46 <option value="sam">sam</option>
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47 <option value="gtf">gtf</option>
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48 </param>
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49 <when value="bed">
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50 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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51 </when>
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52 <when value="gff">
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53 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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54 </when>
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55 <when value="gff2">
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56 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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57 </when>
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58 <when value="gff3">
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59 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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60 </when>
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61 <when value="sam">
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62 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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63 </when>
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64 <when value="gtf">
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65 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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66 </when>
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67 </conditional>
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68
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69 <conditional name="formatType2">
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70 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
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71 <option value="bed">bed</option>
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72 <option value="gff">gff</option>
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73 <option value="gff2">gff2</option>
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74 <option value="gff3">gff3</option>
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75 <option value="sam">sam</option>
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76 <option value="gtf">gtf</option>
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77 </param>
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78 <when value="bed">
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79 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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80 </when>
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81 <when value="gff">
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82 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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83 </when>
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84 <when value="gff2">
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85 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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86 </when>
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87 <when value="gff3">
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88 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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89 </when>
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90 <when value="sam">
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91 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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92 </when>
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93 <when value="gtf">
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94 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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95 </when>
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96 </conditional>
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97
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98 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/>
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99
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100 </inputs>
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101
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102 <outputs>
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103 <data name="outputFileGff" format="gff3" label="[computeCoverage] OUTPUT file"/>
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104 </outputs>
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105
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106 <help>
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107 This tool considers a query and a reference files, and gives the coverage of the query file by the reference. The output file is similar to the query file, where a tag **coverage** has been added.
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108 </help>
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109 </tool>
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110
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