Mercurial > repos > bgruening > deeptools_compute_matrix
annotate computeMatrix.xml @ 2:df1ee352b23b draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 7150f0c106abd56920767518cc331ef6e4e7f439
| author | bgruening |
|---|---|
| date | Thu, 18 Feb 2016 11:53:52 -0500 |
| parents | 275ed3e83de0 |
| children | a842285199d9 |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0"> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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2 <description>prepares data for plotting a heatmap or a profile of given regions</description> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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3 <macros> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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4 <token name="@BINARY@">computeMatrix</token> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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5 <import>deepTools_macros.xml</import> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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6 </macros> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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7 <expand macro="requirements" /> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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8 <command> |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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9 <![CDATA[ |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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10 #import tempfile |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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11 #set bw_files=[] |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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12 #for $counter, $bigwig in enumerate($scoreFileName): |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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13 ln -s "${bigwig}" "file_${counter}.bw" && |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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14 #silent $bw_files.append('file_%s.bw' % $counter) |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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15 #end for |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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16 |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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17 #set bed_files=[] |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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18 #for $counter, $rf in enumerate($regionsFiles): |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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19 ln -s "${rf.regionsFile}" "group_${counter}.bed" && |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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20 #silent $bed_files.append('group_%s.bed' % $counter) |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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21 #end for |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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22 |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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23 @BINARY@ |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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24 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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25 $mode.mode_select |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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26 --regionsFileName '#echo "' '".join($bed_files)#' |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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27 |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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28 --scoreFileName '#echo "' '".join($bw_files)#' |
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275ed3e83de0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
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29 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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30 --outFileName '$outFileName' |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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31 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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32 @THREADS@ |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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33 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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34 #if $output.showOutputSettings == "yes" |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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35 #if $output.saveMatrix: |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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36 --outFileNameMatrix '$outFileNameMatrix' |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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37 #end if |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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38 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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39 #if $output.saveSortedRegions: |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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40 --outFileSortedRegions '$outFileSortedRegions' |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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41 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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42 #end if |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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43 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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44 #if $mode.mode_select == "reference-point": |
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14cb57237e46
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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45 --referencePoint $mode.referencePoint |
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46 $mode.nanAfterEnd |
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47 --beforeRegionStartLength $mode.beforeRegionStartLength |
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48 --afterRegionStartLength $mode.afterRegionStartLength |
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49 #else |
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50 --regionBodyLength $mode.regionBodyLength |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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51 #if $mode.regionStartLength.regionStartLength_select == "yes": |
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52 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength |
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53 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength |
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14cb57237e46
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54 #end if |
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55 #end if |
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56 |
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57 #if $advancedOpt.showAdvancedOpt == "yes": |
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58 --sortRegions '$advancedOpt.sortRegions' |
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59 --sortUsing '$advancedOpt.sortUsing' |
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60 --averageTypeBins '$advancedOpt.averageTypeBins' |
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61 $advancedOpt.skipZeros |
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62 $advancedOpt.missingDataAsZero |
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63 --binSize $advancedOpt.binSize |
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64 |
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65 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '': |
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66 --minThreshold $advancedOpt.minThreshold |
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67 #end if |
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68 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '': |
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69 --maxThreshold $advancedOpt.maxThreshold |
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70 #end if |
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71 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': |
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72 --scale $advancedOpt.scale |
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73 #end if |
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74 |
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75 #end if |
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76 ]]> |
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77 </command> |
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78 <inputs> |
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79 |
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80 <repeat name="regionsFiles" title="Select regions" min="1"> |
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81 <param name="regionsFile" format="bed" type="data" label="Regions to plot" |
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82 help="File, in BED format, containing the regions to plot."/> |
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83 </repeat> |
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84 |
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85 <param name="scoreFileName" format="bigwig" type="data" |
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86 label="Score file" multiple="True" |
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87 help="You can generate a bigWig file from a BAM file using the |
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88 bamCoverage tool. (--scoreFileName)"/> |
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89 |
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90 <conditional name="mode" > |
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91 <param name="mode_select" type="select" |
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92 label="computeMatrix has two main output options" |
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93 help="In the scale-regions mode, all regions in the BED file are |
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94 stretched or shrunken to the same length (in bases) that is indicated |
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95 by the user. Reference-point refers to a position within the BED |
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96 regions (start or end of each region). In the reference-point mode only |
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97 those genomic positions before (upstream) and/or after (downstream) |
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98 the reference point will be considered."> |
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99 <option value="scale-regions" selected="true">scale-regions</option> |
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100 <option value="reference-point">reference-point</option> |
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101 </param> |
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102 |
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103 <when value="scale-regions" > |
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104 <param argument="--regionBodyLength" type="integer" value="500" |
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105 label="Distance in bases to which all regions are going to be fit" help=""/> |
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106 <conditional name="regionStartLength"> |
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107 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> |
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108 <option value="no" selected="true">no</option> |
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109 <option value="yes">yes</option> |
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110 </param> |
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111 <when value="no" /> |
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112 <when value="yes"> |
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113 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1" |
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114 label="Distance upstream of the region start position" |
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115 help="If the regions are genes, this would be the |
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116 distance upstream of the transcription start site."/> |
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117 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1" |
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118 label="Distance downstream of the region end position" |
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119 help="If the regions are genes, this would be the |
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120 distance downstream of the transcription end site."/> |
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121 </when> |
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122 </conditional> |
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123 </when> |
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124 <when value="reference-point"> |
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125 <param name="referencePoint" type="select" label="The reference point for the plotting"> |
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126 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> |
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127 <option value="TES">end of region (e.g. TES)</option> |
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128 <option value="center">center of region</option> |
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129 </param> |
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130 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" |
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131 label="Discard any values after the region end" |
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132 help="This is useful to visualize the region end when not using the |
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133 scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/> |
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134 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" |
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135 label="Distance upstream of the start site of the regions defined in the region file" |
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136 help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/> |
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137 <param name="afterRegionStartLength" type="integer" value="1000" min="1" |
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138 label="Distance downstream of the end site of the given regions" |
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139 help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/> |
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140 </when> |
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141 </conditional> |
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142 |
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143 <expand macro="input_graphic_output_settings"> |
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144 <expand macro="input_save_matrix_values" /> |
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145 </expand> |
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146 |
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147 <conditional name="advancedOpt" > |
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148 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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149 <option value="no" selected="true">no</option> |
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150 <option value="yes">yes</option> |
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151 </param> |
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152 <when value="no" /> |
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153 <when value="yes"> |
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154 <param name="binSize" type="integer" value="50" min="1" |
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155 label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length" |
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156 help="(--binSize)"/> |
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157 |
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158 <expand macro="sortRegions" /> |
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159 <expand macro="sortUsing" /> |
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160 |
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161 <param name="averageTypeBins" type="select" |
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162 label="Define the type of statistic that should be displayed." |
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163 help="The value is computed for each bin. (--averageTypeBins)"> |
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164 <option value="mean" selected="true">mean</option> |
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165 <option value="median">median</option> |
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166 <option value="min">min</option> |
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167 <option value="max">max</option> |
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168 <option value="sum">sum</option> |
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169 <option value="std">std</option> |
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170 </param> |
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171 |
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172 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False" |
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173 label="Convert missing values to 0?" |
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174 help="If set to 'yes', missing values (NAs) are converted |
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175 to 0. If you want to use clustering with plotHeatmap |
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176 or plotProfile, set this to 'yes'. |
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177 The default is to ignore missing values, which will be |
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178 depicted as black areas once a heatmap is created. |
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179 (--missingDataAsZero)" /> |
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180 |
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181 <expand macro="skipZeros" /> |
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182 |
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183 <param name="minThreshold" type="float" optional="True" |
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184 label="Minimum threshold" |
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185 help="Any region containing a value that is equal or less than this numeric |
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186 value will be skipped. This is useful to skip, for example, genes where the |
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187 read count is zero for any of the bins which could be the result of |
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188 unmappable areas and can bias the overall results. (--minThreshold)"/> |
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189 <param name="maxThreshold" type="float" optional="True" |
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190 label="Maximum threshold" |
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191 help="Any region containing a value that is equal or higher that this |
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192 numeric value will be skipped. The max threshold is useful to skip those |
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193 few regions with very high read counts (e.g. major satellites) that may |
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194 bias the average values. (--maxThreshold)"/> |
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195 <param name="scale" type="float" optional="True" label="Scaling factor" |
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196 help="If set, all values are multiplied by this number. (--scale)"/> |
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197 </when> |
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198 </conditional> |
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199 </inputs> |
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200 <outputs> |
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201 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> |
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202 <expand macro="output_graphic_outputs" /> |
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203 <expand macro="output_save_matrix_values" /> |
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204 </outputs> |
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205 <!-- |
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206 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 |
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207 --> |
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208 <tests> |
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209 <test> |
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210 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> |
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211 <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" /> |
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212 <param name="showAdvancedOpt" value="yes" /> |
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213 <param name="mode_select" value="reference-point" /> |
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214 <param name="binSize" value="10" /> |
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215 <param name="sortUsing" value="sum" /> |
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216 <param name="averageTypeBins" value="sum" /> |
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217 <param name="beforeRegionStartLength" value="10" /> |
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218 <param name="afterRegionStartLength" value="10" /> |
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219 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
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220 </test> |
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221 <test> |
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222 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> |
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223 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> |
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224 <param name="showAdvancedOpt" value="yes" /> |
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225 <param name="mode_select" value="reference-point" /> |
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226 <param name="binSize" value="10" /> |
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227 <param name="beforeRegionStartLength" value="10" /> |
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228 <param name="afterRegionStartLength" value="10" /> |
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229 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
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230 </test> |
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231 <test> |
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232 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> |
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233 <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> |
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234 <param name="showAdvancedOpt" value="yes" /> |
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235 <param name="mode_select" value="scale-regions" /> |
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236 <param name="endLabel" value="END" /> |
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237 <param name="regionStartLength" value="yes" /> |
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238 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
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239 </test> |
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240 </tests> |
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241 <help> |
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242 <![CDATA[ |
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243 |
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244 What it does |
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245 ---------------- |
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246 |
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247 This tool prepares an intermediate file (a gzipped table of values) |
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248 that contains scores associated with genomic regions. |
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249 The regions can either be scaled to the same size (using the ``scale-regions`` mode) or you can choose the start, end, or center of each region as the focus point for the score calculations. |
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250 For more details, check out the explanation `here <file:///Users/frd2007/Documents/MPI/deepTools/docs/_build/html/content/tools/computeMatrix.html#details>`_. |
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251 |
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252 The intermediate file produced by ``computeMatrix`` is meant to be used with ``plotHeatmap`` and ``plotProfile``. |
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253 See the descriptions of ``plotHeatmap`` and ``plotProfile`` for example plots. |
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254 |
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255 .. image:: $PATH_TO_IMAGES/computeMatrix_overview.png |
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256 :alt: Relationship between computeMatrix, heatmapper and profiler |
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257 :width: 600 |
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258 :height: 418 |
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259 |
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260 ======= |
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261 |
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262 Usage hints |
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263 ------------- |
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264 |
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265 The supplied genomic regions can really be anything - genes, parts of genes, ChIP-seq peaks, favorite genome regions... as long as you provide a proper file |
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266 in BED or INTERVAL format. If you would like to compare different groups of regions (e.g., genes from chromosome 2 and 3), you can supply more than 1 regions file, one for each group by selecting "Insert Select regions". |
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267 |
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268 .. image:: $PATH_TO_IMAGES/computeMatrix_selectRegions.png |
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269 :width: 600 |
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270 :height: 150 |
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271 |
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272 You can select as many score (bigWig) files as you like. Simply use the Shift and/or Command key while clicking on the files of interest. |
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273 |
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274 .. image:: $PATH_TO_IMAGES/computeMatrix_selectScores.png |
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275 :width: 600 |
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276 :height: 136 |
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277 |
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278 The multitude of parameters can seem daunting at first - here are the options that we tend to tune most often: |
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279 |
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280 * ``bin Size`` -- The default value works well most of the time, but if you want to have a more finely grained image, decrease the default value (but not smaller than your bigWig file(s)' bin size). If you want to reduce the computation time, increase it. |
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281 * ``Skip zeros`` -- useful to avoid completely blank lines in the heatmap. |
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282 * ``Convert missing values to 0?`` -- If you want to identify clusters of similar regions in an unsupervised fashion using ``plotHeatmap`` and/or ``plotProfile``, you should definitely set this to 'yes'. |
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283 |
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284 |
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285 Output files |
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286 --------------- |
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287 |
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288 The default output is a **gzipped table of values** that is used by both ``plotHeatmap`` and ``plotProfile``. |
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289 |
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290 The optional output files include a) the **regions after sorting and filtering (if selected)** as they were used to calculate the values for the plotting, and b) the uncompressed table that **underlies the heatmap**. |
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291 |
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292 **TIP:** ``computeMatrix`` can also be used to filter and sort regions according to their score by making use of the "advanced output settings". |
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293 |
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294 .. image:: $PATH_TO_IMAGES/computeMatrix_advancedOutput.png |
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295 :width: 600 |
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296 :height: 189 |
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297 |
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298 .. image:: $PATH_TO_IMAGES/computeMatrix_output.png |
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299 :width: 600 |
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300 :height: 297 |
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301 |
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302 Note that these advanced output options are available for ``plotHeatmap`` and ``plotProfile``, too. |
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303 |
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304 See the following table for the optional output options: |
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305 |
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306 +-----------------------------------+--------------------+-----------------+-----------------+ |
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307 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** | |
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308 +-----------------------------------+--------------------+-----------------+-----------------+ |
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309 | values underlying the heatmap | yes | yes | no | |
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310 +-----------------------------------+--------------------+-----------------+-----------------+ |
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311 | values underlying the profile | no | no | yes | |
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312 +-----------------------------------+--------------------+-----------------+-----------------+ |
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313 | sorted and/or filtered regions | yes | yes | yes | |
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314 +-----------------------------------+--------------------+-----------------+-----------------+ |
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315 |
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316 **More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_. |
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317 |
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318 ----- |
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319 |
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320 @REFERENCES@ |
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321 ]]> |
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322 </help> |
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323 <expand macro="citations" /> |
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324 </tool> |