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1 <tool id="clusterizeBySlidingWindows" name="clusterize By SlidingWindows">
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2 <description>Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region) and keep only highest peaks.</description>
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3 <command interpreter="python">
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4 ../Java/Python/clusterizeBySlidingWindows.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 == 'sam':
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14 -f sam
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15 #elif $formatType.FormatInputFileName == 'gtf':
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16 -f gtf
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17 #end if
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18 -s $size
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19 -e $overlap
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20 -o $outputFileGff
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21 $normalize
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22 $strands
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23
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24 #if $OptionTag.tag == "Yes":
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25 -g $OptionTag.value
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26 #end if
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27
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28 #if $OptionsOperation.operation == "Yes":
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29 -r $OptionsOperation.value
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30 #end if
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31
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32 #if $OptionWriteTag.writeTag == "Yes":
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33 -w $OptionWriteTag.value
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34 #end if
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35
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36 $strand
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37 $plot $plotPng
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38 $excel $excelOutput
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39
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40
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41 </command>
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42
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43 <inputs>
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44 <conditional name="formatType">
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45 <param name="FormatInputFileName" type="select" label="Input File Format">
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46 <option value="bed">bed</option>
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47 <option value="gff">gff</option>
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48 <option value="gff2">gff2</option>
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49 <option value="gff3">gff3</option>
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50 <option value="sam">sam</option>
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51 <option value="gtf">gtf</option>
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52 </param>
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53 <when value="bed">
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54 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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55 </when>
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56 <when value="gff">
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57 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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58 </when>
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59 <when value="gff2">
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60 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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61 </when>
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62 <when value="gff3">
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63 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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64 </when>
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65 <when value="sam">
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66 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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67 </when>
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68 <when value="gtf">
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69 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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70 </when>
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71 </conditional>
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72
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73
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74 <param name="size" type="text" value="50000" label="Size option" help="Size of the regions."/>
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75 <param name="overlap" type="text" value="50" label="Overlap option" help="Overlap between two consecutive regions."/>
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76 <param name="normalize" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Normalize option for only GFF3 file format" help="This option normalizes (Warning!! Only for GFF3 file!)"/>
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77 <param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strands option" help="Consider the two strands separately."/>
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78
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79 <conditional name="OptionTag">
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80 <param name="tag" type="select" label="use a given tag as input (instead of summing number of features)">
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81 <option value="Yes">Yes</option>
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82 <option value="No" selected="true">No</option>
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83 </param>
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84 <when value="Yes">
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85 <param name="value" type="text" value="None" label="tag option" help="write a tag name you want to observe."/>
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86 </when>
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87 <when value="No">
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88 </when>
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89 </conditional>
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90
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91
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92 <conditional name="OptionsOperation">
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93 <param name="operation" type="select" label="combine tag value with given operation [choice (sum, avg, med, min, max)]">
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94 <option value="Yes">Yes</option>
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95 <option value="No" selected="true">No</option>
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96 </param>
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97 <when value="Yes">
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98 <param name="value" type="text" value="None" label="operation option" help="You can ONLY choose one of fowlling operation : sum, avg, med, min, max."/>
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99 </when>
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100 <when value="No">
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101 </when>
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102 </conditional>
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103
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104
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105 <conditional name="OptionWriteTag">
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106 <param name="writeTag" type="select" label="write a new tag in output file">
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107 <option value="Yes">Yes</option>
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108 <option value="No" selected="true">No</option>
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109 </param>
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110 <when value="Yes">
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111 <param name="value" type="text" value="nbElements" label="write tag option" help="print the result in the given tag (default usually is 'nbElements')"/>
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112 </when>
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113 <when value="No">
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114 </when>
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115 </conditional>
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116
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117 <param name="strand" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strand option" help="This option considers the two strands separately."/>
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118 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="This option creates a png file."/>
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119 <param name="excel" type="boolean" truevalue="-x" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
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120
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121 </inputs>
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122
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123 <outputs>
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124 <data name="outputFileGff" format="gff3"/>
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125 <data name="excelOutput" format="csv">
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126 <filter>excel</filter>
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127 </data>
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128 <data name="plotPng" format="png">
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129 <filter>plot</filter>
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130 </data>
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131 </outputs>
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132 </tool>
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