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+ − 1 <tool id="GetDifferentialExpression" name="get differential expression">
+ − 2 <description>Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.</description>
+ − 3 <command interpreter="python">
+ − 4 ../Java/Python/GetDifferentialExpression.py -i $formatType.inputFileName1
+ − 5 #if $formatType.FormatInputFileName1 == 'bed':
+ − 6 -f bed
+ − 7 #elif $formatType.FormatInputFileName1 == 'gff':
+ − 8 -f gff
+ − 9 #elif $formatType.FormatInputFileName1 == 'gff2':
+ − 10 -f gff2
+ − 11 #elif $formatType.FormatInputFileName1 == 'gff3':
+ − 12 -f gff3
+ − 13 #elif $formatType.FormatInputFileName1 == 'sam':
+ − 14 -f sam
+ − 15 #elif $formatType.FormatInputFileName1 == 'gtf':
+ − 16 -f gtf
+ − 17 #end if
+ − 18
+ − 19 -j $formatType2.inputFileName2
+ − 20 #if $formatType2.FormatInputFileName2 == 'bed':
+ − 21 -g bed
+ − 22 #elif $formatType2.FormatInputFileName2 == 'gff':
+ − 23 -g gff
+ − 24 #elif $formatType2.FormatInputFileName2 == 'gff2':
+ − 25 -g gff2
+ − 26 #elif $formatType2.FormatInputFileName2 == 'gff3':
+ − 27 -g gff3
+ − 28 #elif $formatType2.FormatInputFileName2 == 'sam':
+ − 29 -g sam
+ − 30 #elif $formatType2.FormatInputFileName2 == 'gtf':
+ − 31 -g gtf
+ − 32 #end if
+ − 33
+ − 34 -k $formatTypeRef.inputFileNameRef
+ − 35 #if $formatTypeRef.FormatInputFileNameRef == 'bed':
+ − 36 -l bed
+ − 37 #elif $formatTypeRef.FormatInputFileNameRef == 'gff':
+ − 38 -l gff
+ − 39 #elif $formatTypeRef.FormatInputFileNameRef == 'gff2':
+ − 40 -l gff2
+ − 41 #elif $formatTypeRef.FormatInputFileNameRef == 'gff3':
+ − 42 -l gff3
+ − 43 #elif $formatTypeRef.FormatInputFileNameRef == 'sam':
+ − 44 -l sam
+ − 45 #elif $formatTypeRef.FormatInputFileNameRef == 'gtf':
+ − 46 -l gtf
+ − 47 #end if
+ − 48
+ − 49 -o $outputFileGff
+ − 50
+ − 51 $simple
+ − 52 $adjusted
+ − 53
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+ − 54
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+ − 55 #if $optionSimplePara.simplePara == 'Yes':
+ − 56 -S $optionSimplePara.paraValue
+ − 57 #end if
+ − 58
+ − 59 #if $optionFixedSizeFactor.FSF == 'Yes':
+ − 60 -x $optionFixedSizeFactor.FSFValue
+ − 61 #end if
+ − 62
+ − 63 #if $optionFDR.FDR == 'Yes':
+ − 64 -d $optionFDR.FDRValue
+ − 65 #end if
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+ − 66 $plot $outputFilePNG
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+ − 67 </command>
+ − 68
+ − 69 <inputs>
+ − 70 <conditional name="formatType">
+ − 71 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
+ − 72 <option value="bed">bed</option>
+ − 73 <option value="gff">gff</option>
+ − 74 <option value="gff2">gff2</option>
+ − 75 <option value="gff3">gff3</option>
+ − 76 <option value="sam">sam</option>
+ − 77 <option value="gtf">gtf</option>
+ − 78 </param>
+ − 79 <when value="bed">
+ − 80 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
+ − 81 </when>
+ − 82 <when value="gff">
+ − 83 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
+ − 84 </when>
+ − 85 <when value="gff2">
+ − 86 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
+ − 87 </when>
+ − 88 <when value="gff3">
+ − 89 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
+ − 90 </when>
+ − 91 <when value="sam">
+ − 92 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
+ − 93 </when>
+ − 94 <when value="gtf">
+ − 95 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
+ − 96 </when>
+ − 97 </conditional>
+ − 98
+ − 99 <conditional name="formatType2">
+ − 100 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
+ − 101 <option value="bed">bed</option>
+ − 102 <option value="gff">gff</option>
+ − 103 <option value="gff2">gff2</option>
+ − 104 <option value="gff3">gff3</option>
+ − 105 <option value="sam">sam</option>
+ − 106 <option value="gtf">gtf</option>
+ − 107 </param>
+ − 108 <when value="bed">
+ − 109 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
+ − 110 </when>
+ − 111 <when value="gff">
+ − 112 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
+ − 113 </when>
+ − 114 <when value="gff2">
+ − 115 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
+ − 116 </when>
+ − 117 <when value="gff3">
+ − 118 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
+ − 119 </when>
+ − 120 <when value="sam">
+ − 121 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
+ − 122 </when>
+ − 123 <when value="gtf">
+ − 124 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
+ − 125 </when>
+ − 126 </conditional>
+ − 127
+ − 128 <conditional name="formatTypeRef">
+ − 129 <param name="FormatInputFileNameRef" type="select" label="Input Ref File Format ">
+ − 130 <option value="bed">bed</option>
+ − 131 <option value="gff">gff</option>
+ − 132 <option value="gff2">gff2</option>
+ − 133 <option value="gff3">gff3</option>
+ − 134 <option value="sam">sam</option>
+ − 135 <option value="gtf">gtf</option>
+ − 136 </param>
+ − 137 <when value="bed">
+ − 138 <param name="inputFileNameRef" format="bed" type="data" label="Input Ref File"/>
+ − 139 </when>
+ − 140 <when value="gff">
+ − 141 <param name="inputFileNameRef" format="gff" type="data" label="Input Ref File"/>
+ − 142 </when>
+ − 143 <when value="gff2">
+ − 144 <param name="inputFileNameRef" format="gff2" type="data" label="Input Ref File"/>
+ − 145 </when>
+ − 146 <when value="gff3">
+ − 147 <param name="inputFileNameRef" format="gff3" type="data" label="Input Ref File"/>
+ − 148 </when>
+ − 149 <when value="sam">
+ − 150 <param name="inputFileNameRef" format="sam" type="data" label="Input Ref File"/>
+ − 151 </when>
+ − 152 <when value="gtf">
+ − 153 <param name="inputFileNameRef" format="gtf" type="data" label="Input Ref File"/>
+ − 154 </when>
+ − 155 </conditional>
+ − 156
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+ − 157 <param name="simple" type="boolean" truevalue="-s" falsevalue="" checked="false" label="normalize using the number of reads in each condition"/>
+ − 158 <param name="adjusted" type="boolean" truevalue="-a" falsevalue="" checked="false" label="normalize using the number of reads of 'mean' regions"/>
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+ − 159
+ − 160 <conditional name="optionSimplePara">
+ − 161 <param name="simplePara" type="select" label="provide the number of reads" >
+ − 162 <option value="Yes">Yes</option>
+ − 163 <option value="No" selected="true">No</option>
+ − 164 </param>
+ − 165 <when value="Yes">
+ − 166 <param name="paraValue" type="text" value="None" label="provide the number of reads" />
+ − 167 </when>
+ − 168 <when value="No">
+ − 169 </when>
+ − 170 </conditional>
+ − 171
+ − 172 <conditional name="optionFixedSizeFactor">
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+ − 173 <param name="FSF" type="select" label="give the magnification factor for the normalization using fixed size sliding windows in reference regions (leave empty for no such normalization)">
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+ − 174 <option value="Yes">Yes</option>
+ − 175 <option value="No" selected="true">No</option>
+ − 176 </param>
+ − 177 <when value="Yes">
+ − 178 <param name="FSFValue" type="integer" value="0" />
+ − 179 </when>
+ − 180 <when value="No">
+ − 181 </when>
+ − 182 </conditional>
+ − 183
+ − 184 <conditional name="optionFDR">
+ − 185 <param name="FDR" type="select" label="use FDR">
+ − 186 <option value="Yes">Yes</option>
+ − 187 <option value="No" selected="true">No</option>
+ − 188 </param>
+ − 189 <when value="Yes">
+ − 190 <param name="FDRValue" type="float" value="0.0"/>
+ − 191 </when>
+ − 192 <when value="No">
+ − 193 </when>
+ − 194 </conditional>
+ − 195
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+ − 196 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="plot cloud plot"/>
+ − 197
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+ − 198 </inputs>
+ − 199
+ − 200 <outputs>
+ − 201 <data name="outputFileGff" format="gff3" label="[GetDifferentialExpression]out file"/>
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+ − 202 <data name="outputFilePNG" format="PNG" label="[GetDifferentialExpression]PNG file">
+ − 203 <filter>plot</filter>
+ − 204 </data>
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+ − 205 </outputs>
+ − 206
+ − 207 <help>
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+ − 208 example: python GetDifferentialExpression.py -i input1 -f gff3 -j input2 -g gff3 -k ref -l gff3 -o output.gff3
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+ − 209 </help>
+ − 210 </tool>
