Mercurial > repos > bgruening > deeptools_compute_matrix_operations
comparison computeMatrixOperations.xml @ 16:39ba04eacd0f draft
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"
| author | bgruening |
|---|---|
| date | Fri, 11 Feb 2022 10:02:59 +0000 |
| parents | fd7e4d6a5d68 |
| children | 42402233f300 |
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| 15:f9a231be10dc | 16:39ba04eacd0f |
|---|---|
| 69 #silent $files.append(str($f.regionsFile)) | 69 #silent $files.append(str($f.regionsFile)) |
| 70 #end for | 70 #end for |
| 71 -m $submodule.matrixFile | 71 -m $submodule.matrixFile |
| 72 -R '#echo "' '".join($files)#' | 72 -R '#echo "' '".join($files)#' |
| 73 -o $outFileName | 73 -o $outFileName |
| 74 #else if $submodule.command == "dataRange": | |
| 75 dataRange | |
| 76 -m $submodule.matrixFile | |
| 77 > $outFileTxt | |
| 74 #end if | 78 #end if |
| 75 ]]> | 79 ]]> |
| 76 </command> | 80 </command> |
| 77 <inputs> | 81 <inputs> |
| 78 <conditional name="submodule"> | 82 <conditional name="submodule"> |
| 83 <option value="filterStrand">Filter by strand (filterStrand)</option> | 87 <option value="filterStrand">Filter by strand (filterStrand)</option> |
| 84 <option value="filterValues">Filter by min/max value (filterValues)</option> | 88 <option value="filterValues">Filter by min/max value (filterValues)</option> |
| 85 <option value="rbind">Bind matrices, top to bottom (rbind)</option> | 89 <option value="rbind">Bind matrices, top to bottom (rbind)</option> |
| 86 <option value="cbind">Bind matrices, left to right (cbind)</option> | 90 <option value="cbind">Bind matrices, left to right (cbind)</option> |
| 87 <option value="sort">Sort by region order in specified files (sort)</option> | 91 <option value="sort">Sort by region order in specified files (sort)</option> |
| 92 <option value="dataRange">Returns the min, max, median, 10th and 90th percentile of the matrix values per sample (dataRange)</option> | |
| 88 </param> | 93 </param> |
| 89 <when value="info"> | 94 <when value="info"> |
| 90 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" | 95 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" |
| 91 label="Matrix file from the computeMatrix tool" help=""/> | 96 label="Matrix file from the computeMatrix tool" help=""/> |
| 92 </when> | 97 </when> |
| 148 label="Matrix file from the computeMatrix tool" help=""/> | 153 label="Matrix file from the computeMatrix tool" help=""/> |
| 149 <repeat name="regionsFiles" title="BED or GTF files of regions" min="1"> | 154 <repeat name="regionsFiles" title="BED or GTF files of regions" min="1"> |
| 150 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" | 155 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" |
| 151 help="File, in BED format, containing the regions to plot."/> | 156 help="File, in BED format, containing the regions to plot."/> |
| 152 </repeat> | 157 </repeat> |
| 158 </when> | |
| 159 | |
| 160 <when value="dataRange"> | |
| 161 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" | |
| 162 label="Matrix file from the computeMatrix tool" help=""/> | |
| 153 </when> | 163 </when> |
| 154 </conditional> | 164 </conditional> |
| 155 </inputs> | 165 </inputs> |
| 156 <outputs> | 166 <outputs> |
| 157 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}"> | 167 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}"> |
| 203 +----------------+--------------------------------------------------------------------------------------------------------------------------+ | 213 +----------------+--------------------------------------------------------------------------------------------------------------------------+ |
| 204 + cbind | Merges multiple matrices, left to right. | | 214 + cbind | Merges multiple matrices, left to right. | |
| 205 +----------------+--------------------------------------------------------------------------------------------------------------------------+ | 215 +----------------+--------------------------------------------------------------------------------------------------------------------------+ |
| 206 + sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). | | 216 + sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). | |
| 207 +----------------+--------------------------------------------------------------------------------------------------------------------------+ | 217 +----------------+--------------------------------------------------------------------------------------------------------------------------+ |
| 208 | 218 + dataRange | Returns the min, max, median, 10th and 90th percentile of the matrix values per sample. | |
| 219 +----------------+--------------------------------------------------------------------------------------------------------------------------+ | |
| 209 | 220 |
| 210 These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file. | 221 These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file. |
| 211 | 222 |
| 212 ----- | 223 ----- |
| 213 | 224 |