Mercurial > repos > yufei-luo > differential_expression_analysis_pipeline_for_rnaseq_data
comparison deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/compareOverlapping_parallel.xml @ 10:6e573fd3c41b draft
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| author | yufei-luo |
|---|---|
| date | Mon, 13 May 2013 10:06:30 -0400 |
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| 9:a03838a6eb54 | 10:6e573fd3c41b |
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| 1 <tool id="CompareOverlapping_parallel" name="CompareOverlapping_parallel"> | |
| 2 <description>Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes.</description> | |
| 3 <command interpreter="python"> | |
| 4 compareOverlapping_parallel.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 --inputTxt $inputTxt | |
| 20 | |
| 21 -g $format2 | |
| 22 | |
| 23 --outTxt $outTxtFile | |
| 24 | |
| 25 #if $optionNFirstFile1.NFirstForFile1 == 'Yes': | |
| 26 -S $optionNFirstFile1.firstNtFile1 | |
| 27 #end if | |
| 28 #if $optionNFirstFile2.NFirstForFile2 == 'Yes': | |
| 29 -s $optionNFirstFile2.firstNtFile2 | |
| 30 #end if | |
| 31 #if $optionNLastFile1.NLastForFile1 == 'Yes': | |
| 32 -U $optionNLastFile1.lastNtFile1 | |
| 33 #end if | |
| 34 #if $optionNLastFile2.NLastForFile2 == 'Yes': | |
| 35 -u $optionNLastFile2.lastNtFile2 | |
| 36 #end if | |
| 37 | |
| 38 #if $optionExtentionCinqFile1.extentionFile1 == 'Yes': | |
| 39 -E $optionExtentionCinqFile1.extention51 | |
| 40 #end if | |
| 41 #if $optionExtentionCinqFile2.extentionFile2 == 'Yes': | |
| 42 -e $optionExtentionCinqFile2.extention52 | |
| 43 #end if | |
| 44 | |
| 45 #if $optionExtentionTroisFile1.extentionFile1 == 'Yes': | |
| 46 -N $optionExtentionTroisFile1.extention31 | |
| 47 #end if | |
| 48 #if $optionExtentionTroisFile2.extentionFile2 == 'Yes': | |
| 49 -n $optionExtentionTroisFile2.extention32 | |
| 50 #end if | |
| 51 | |
| 52 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear': | |
| 53 -c | |
| 54 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': | |
| 55 -a | |
| 56 #end if | |
| 57 | |
| 58 #if $OptionDistance.Dist == 'Yes': | |
| 59 -d $OptionDistance.distance | |
| 60 #end if | |
| 61 | |
| 62 #if $OptionMinOverlap.MO == 'Yes': | |
| 63 -m $OptionMinOverlap.minOverlap | |
| 64 #end if | |
| 65 | |
| 66 $InvertMatch | |
| 67 $ReportIntron | |
| 68 $NotOverlapping | |
| 69 $tar $outputTarFile | |
| 70 </command> | |
| 71 | |
| 72 <inputs> | |
| 73 | |
| 74 <conditional name="formatType"> | |
| 75 <param name="FormatInputFileName1" type="select" label="Input File Format 1"> | |
| 76 <option value="bed">bed</option> | |
| 77 <option value="gff">gff</option> | |
| 78 <option value="gff2">gff2</option> | |
| 79 <option value="gff3">gff3</option> | |
| 80 <option value="sam">sam</option> | |
| 81 <option value="gtf">gtf</option> | |
| 82 </param> | |
| 83 <when value="bed"> | |
| 84 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/> | |
| 85 </when> | |
| 86 <when value="gff"> | |
| 87 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/> | |
| 88 </when> | |
| 89 <when value="gff2"> | |
| 90 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/> | |
| 91 </when> | |
| 92 <when value="gff3"> | |
| 93 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/> | |
| 94 </when> | |
| 95 <when value="sam"> | |
| 96 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/> | |
| 97 </when> | |
| 98 <when value="gtf"> | |
| 99 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> | |
| 100 </when> | |
| 101 </conditional> | |
| 102 | |
| 103 <param name="inputTxt" type="data" format="txt" label="A txt file contains a list of several input transcripts files." /> | |
| 104 | |
| 105 <param name="format2" type="text" value="bed" label="format for File 2, you can choose [bed, gff, gff2, gff3, sam, gtf]"/> | |
| 106 | |
| 107 <conditional name="optionNFirstFile1"> | |
| 108 <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1"> | |
| 109 <option value="Yes">Yes</option> | |
| 110 <option value="No" selected="true">No</option> | |
| 111 </param> | |
| 112 <when value="Yes"> | |
| 113 <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" /> | |
| 114 </when> | |
| 115 <when value="No"> | |
| 116 </when> | |
| 117 </conditional> | |
| 118 <conditional name="optionNFirstFile2"> | |
| 119 <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2"> | |
| 120 <option value="Yes">Yes</option> | |
| 121 <option value="No" selected="true">No</option> | |
| 122 </param> | |
| 123 <when value="Yes"> | |
| 124 <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" /> | |
| 125 </when> | |
| 126 <when value="No"> | |
| 127 </when> | |
| 128 </conditional> | |
| 129 | |
| 130 <conditional name="optionNLastFile1"> | |
| 131 <param name="NLastForFile1" type="select" label="NLast for file 1"> | |
| 132 <option value="Yes">Yes</option> | |
| 133 <option value="No" selected="true">No</option> | |
| 134 </param> | |
| 135 <when value="Yes"> | |
| 136 <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/> | |
| 137 </when> | |
| 138 <when value="No"> | |
| 139 </when> | |
| 140 </conditional> | |
| 141 <conditional name="optionNLastFile2"> | |
| 142 <param name="NLastForFile2" type="select" label="NLast for file 2"> | |
| 143 <option value="Yes">Yes</option> | |
| 144 <option value="No" selected="true">No</option> | |
| 145 </param> | |
| 146 <when value="Yes"> | |
| 147 <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/> | |
| 148 </when> | |
| 149 <when value="No"> | |
| 150 </when> | |
| 151 </conditional> | |
| 152 | |
| 153 <conditional name="optionExtentionCinqFile1"> | |
| 154 <param name="extentionFile1" type="select" label="Extension towards 5 for file 1"> | |
| 155 <option value="Yes">Yes</option> | |
| 156 <option value="No" selected="true">No</option> | |
| 157 </param> | |
| 158 <when value="Yes"> | |
| 159 <param name="extention51" type="integer" value="1" label="in file 1" /> | |
| 160 </when> | |
| 161 <when value="No"> | |
| 162 </when> | |
| 163 </conditional> | |
| 164 | |
| 165 <conditional name="optionExtentionCinqFile2"> | |
| 166 <param name="extentionFile2" type="select" label="Extension towards 5 for file 2"> | |
| 167 <option value="Yes">Yes</option> | |
| 168 <option value="No" selected="true">No</option> | |
| 169 </param> | |
| 170 <when value="Yes"> | |
| 171 <param name="extention52" type="integer" value="1" label="in file 2"/> | |
| 172 </when> | |
| 173 <when value="No"> | |
| 174 </when> | |
| 175 </conditional> | |
| 176 | |
| 177 <conditional name="optionExtentionTroisFile1"> | |
| 178 <param name="extentionFile1" type="select" label="Extension towards 3 for file 1"> | |
| 179 <option value="Yes">Yes</option> | |
| 180 <option value="No" selected="true">No</option> | |
| 181 </param> | |
| 182 <when value="Yes"> | |
| 183 <param name="extention31" type="integer" value="1" label="in file 1" /> | |
| 184 </when> | |
| 185 <when value="No"> | |
| 186 </when> | |
| 187 </conditional> | |
| 188 | |
| 189 <conditional name="optionExtentionTroisFile2"> | |
| 190 <param name="extentionFile2" type="select" label="Extension towards 3 for file 2"> | |
| 191 <option value="Yes">Yes</option> | |
| 192 <option value="No" selected="true">No</option> | |
| 193 </param> | |
| 194 <when value="Yes"> | |
| 195 <param name="extention32" type="integer" value="1" label="in file 2" /> | |
| 196 </when> | |
| 197 <when value="No"> | |
| 198 </when> | |
| 199 </conditional> | |
| 200 | |
| 201 <conditional name="OptionColinearOrAntiSens"> | |
| 202 <param name="OptionCA" type="select" label="Colinear or anti-sens"> | |
| 203 <option value="Colinear">Colinear</option> | |
| 204 <option value="AntiSens">AntiSens</option> | |
| 205 <option value="NONE" selected="true">NONE</option> | |
| 206 </param> | |
| 207 <when value="Colinear"> | |
| 208 </when> | |
| 209 <when value="AntiSens"> | |
| 210 </when> | |
| 211 <when value="NONE"> | |
| 212 </when> | |
| 213 </conditional> | |
| 214 | |
| 215 <conditional name="OptionDistance"> | |
| 216 <param name="Dist" type="select" label="Maximum Distance between two reads"> | |
| 217 <option value="Yes">Yes</option> | |
| 218 <option value="No" selected="true">No</option> | |
| 219 </param> | |
| 220 <when value="Yes"> | |
| 221 <param name="distance" type="integer" value="0"/> | |
| 222 </when> | |
| 223 <when value="No"> | |
| 224 </when> | |
| 225 </conditional> | |
| 226 | |
| 227 <conditional name="OptionMinOverlap"> | |
| 228 <param name="MO" type="select" label="Minimum number of overlapping between two reads"> | |
| 229 <option value="Yes">Yes</option> | |
| 230 <option value="No" selected="true">No</option> | |
| 231 </param> | |
| 232 <when value="Yes"> | |
| 233 <param name="minOverlap" type="integer" value="1"/> | |
| 234 </when> | |
| 235 <when value="No"> | |
| 236 </when> | |
| 237 </conditional> | |
| 238 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/> | |
| 239 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/> | |
| 240 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/> | |
| 241 <param name="tar" type="boolean" truevalue="--tar" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." /> | |
| 242 </inputs> | |
| 243 | |
| 244 <outputs> | |
| 245 <data name="outTxtFile" format="txt" label="overlapping output files "/> | |
| 246 <data name="outputTarFile" format="tar"> | |
| 247 <filter>tar</filter> | |
| 248 </data> | |
| 249 </outputs> | |
| 250 | |
| 251 </tool> |