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+ − 1 <tool id="clusterizeBySlidingWindows" name="clusterize By SlidingWindows">
+ − 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">
+ − 4 ../Java/Python/clusterizeBySlidingWindows.py -i $formatType.inputFileName
+ − 5 #if $formatType.FormatInputFileName == 'bed':
+ − 6 -f bed
+ − 7 #elif $formatType.FormatInputFileName == 'gff':
+ − 8 -f gff
+ − 9 #elif $formatType.FormatInputFileName == 'gff2':
+ − 10 -f gff2
+ − 11 #elif $formatType.FormatInputFileName == 'gff3':
+ − 12 -f gff3
+ − 13 #elif $formatType.FormatInputFileName == 'sam':
+ − 14 -f sam
+ − 15 #elif $formatType.FormatInputFileName == 'gtf':
+ − 16 -f gtf
+ − 17 #end if
+ − 18 -s $size
+ − 19 -e $overlap
+ − 20 -o $outputFileGff
+ − 21 $normalize
+ − 22 $strands
+ − 23
+ − 24 #if $OptionTag.tag == "Yes":
+ − 25 -g $OptionTag.value
+ − 26 #end if
+ − 27
+ − 28 #if $OptionsOperation.operation == "Yes":
+ − 29 -r $OptionsOperation.value
+ − 30 #end if
+ − 31
+ − 32 #if $OptionWriteTag.writeTag == "Yes":
+ − 33 -w $OptionWriteTag.value
+ − 34 #end if
+ − 35
+ − 36 $strand
+ − 37 $plot $plotPng
+ − 38 $excel $excelOutput
+ − 39
+ − 40
+ − 41 </command>
+ − 42
+ − 43 <inputs>
+ − 44 <conditional name="formatType">
+ − 45 <param name="FormatInputFileName" type="select" label="Input File Format">
+ − 46 <option value="bed">bed</option>
+ − 47 <option value="gff">gff</option>
+ − 48 <option value="gff2">gff2</option>
+ − 49 <option value="gff3">gff3</option>
+ − 50 <option value="sam">sam</option>
+ − 51 <option value="gtf">gtf</option>
+ − 52 </param>
+ − 53 <when value="bed">
+ − 54 <param name="inputFileName" format="bed" type="data" label="Input File"/>
+ − 55 </when>
+ − 56 <when value="gff">
+ − 57 <param name="inputFileName" format="gff" type="data" label="Input File"/>
+ − 58 </when>
+ − 59 <when value="gff2">
+ − 60 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
+ − 61 </when>
+ − 62 <when value="gff3">
+ − 63 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
+ − 64 </when>
+ − 65 <when value="sam">
+ − 66 <param name="inputFileName" format="sam" type="data" label="Input File"/>
+ − 67 </when>
+ − 68 <when value="gtf">
+ − 69 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
+ − 70 </when>
+ − 71 </conditional>
+ − 72
+ − 73
+ − 74 <param name="size" type="text" value="50000" label="Size option" help="Size of the regions."/>
+ − 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!)"/>
+ − 77 <param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strands option" help="Consider the two strands separately."/>
6
+ − 78
+ − 79 <conditional name="OptionTag">
31
+ − 80 <param name="tag" type="select" label="use a given tag as input (instead of summing number of features)">
6
+ − 81 <option value="Yes">Yes</option>
+ − 82 <option value="No" selected="true">No</option>
+ − 83 </param>
+ − 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."/>
6
+ − 86 </when>
+ − 87 <when value="No">
+ − 88 </when>
+ − 89 </conditional>
+ − 90
+ − 91
+ − 92 <conditional name="OptionsOperation">
31
+ − 93 <param name="operation" type="select" label="combine tag value with given operation [choice (sum, avg, med, min, max)]">
6
+ − 94 <option value="Yes">Yes</option>
+ − 95 <option value="No" selected="true">No</option>
+ − 96 </param>
+ − 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."/>
6
+ − 99 </when>
+ − 100 <when value="No">
+ − 101 </when>
+ − 102 </conditional>
+ − 103
+ − 104
+ − 105 <conditional name="OptionWriteTag">
+ − 106 <param name="writeTag" type="select" label="write a new tag in output file">
+ − 107 <option value="Yes">Yes</option>
+ − 108 <option value="No" selected="true">No</option>
+ − 109 </param>
+ − 110 <when value="Yes">
+ − 111 <param name="value" type="text" value="nbElements" label="write tag option" help="print the result in the given tag (default usually is 'nbElements')"/>
+ − 112 </when>
+ − 113 <when value="No">
+ − 114 </when>
+ − 115 </conditional>
+ − 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."/>
+ − 118 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="This option creates a png file."/>
+ − 119 <param name="excel" type="boolean" truevalue="-x" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
+ − 120
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+ − 121 </inputs>
+ − 122
+ − 123 <outputs>
+ − 124 <data name="outputFileGff" format="gff3"/>
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+ − 125 <data name="excelOutput" format="csv">
+ − 126 <filter>excel</filter>
+ − 127 </data>
+ − 128 <data name="plotPng" format="png">
+ − 129 <filter>plot</filter>
+ − 130 </data>
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+ − 131 </outputs>
+ − 132 </tool>
