Mercurial > repos > bgruening > deeptools_compute_matrix_operations

comparison computeMatrixOperations.xml @ 17:be95d48dd27f draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
author bgruening
date Fri, 11 Feb 2022 15:57:22 +0000
parents 848ce8f81e6e
children 7ef978dc1b8a
comparison
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16:ee3a1b0f45f1 17:be95d48dd27f
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