Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/GetDifferentialExpression.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
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| children |
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| -1:000000000000 | 0:e0f8dcca02ed |
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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 | |
| 54 | |
| 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 | |
| 66 $plot $outputFilePNG | |
| 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 | |
| 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"/> | |
| 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"> | |
| 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)"> | |
| 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 | |
| 196 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="plot cloud plot"/> | |
| 197 | |
| 198 </inputs> | |
| 199 | |
| 200 <outputs> | |
| 201 <data name="outputFileGff" format="gff3" label="[GetDifferentialExpression]out file"/> | |
| 202 <data name="outputFilePNG" format="PNG" label="[GetDifferentialExpression]PNG file"> | |
| 203 <filter>plot</filter> | |
| 204 </data> | |
| 205 </outputs> | |
| 206 | |
| 207 <help> | |
| 208 example: python GetDifferentialExpression.py -i input1 -f gff3 -j input2 -g gff3 -k ref -l gff3 -o output.gff3 | |
| 209 </help> | |
| 210 </tool> |