Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

annotate hicBuildMatrix.xml @ 19:9edf8894a22d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:12:54 +0000
parents 231687cac31b
children ed2cca6b5de4
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19
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
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1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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495ae38f6e0d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
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2 <description>create a contact matrix</description>
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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3 <macros>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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4 <token name="@BINARY@">hicBuildMatrix</token>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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5 <import>macros.xml</import>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 </macros>
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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7 <expand macro="requirements">
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8bf84c4cb1cb "planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
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8 <requirement type="package" version="1.9">samtools</requirement>
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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9 </expand>
2
eb0d14cdf8b8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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10 <command detect_errors="exit_code"><![CDATA[
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 mkdir ./QCfolder &&
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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13 mkdir '$qc.files_path' &&
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4b85ea34afae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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14 @BINARY@
0
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15 --samFiles
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16 #for $repeat in $samFiles:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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17 '${repeat.samFile}'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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18 #end for
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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19
19
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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20 --restrictionCutFile '$restrictionCutFile'
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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22 #if $restrictionSequence:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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23 --restrictionSequence '$restrictionSequence'
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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24 #end if
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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25 #if $danglingSequence:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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26 --danglingSequence '$danglingSequence'
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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27 #end if
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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28 #if $minDistance:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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29 --minDistance $minDistance
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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30 #end if
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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31 #if $maxLibraryInsertSize:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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32 --maxLibraryInsertSize $maxLibraryInsertSize
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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33 #end if
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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35 #if $binSizes:
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36 --binSize
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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37 #for $repeat in $binSizes
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4b85ea34afae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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38 '${repeat.binSize}'
4b85ea34afae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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39 #end for
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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40 #end if
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41
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iuc
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42 --genomeAssembly $samFiles[0].samFile.metadata.dbkey
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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43
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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44 #if $region:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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45 --region '$region'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 #end if
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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47
7
be42758f532e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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48 --outFileName matrix.$outputFormat
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49
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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50 #if $outBam:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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51 $outBam ./unsorted.bam
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52 #end if
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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53
2
eb0d14cdf8b8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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54 $keepSelfCircles
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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55 $removeSelfLigation
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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56 $skipDuplicationCheck
0
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57
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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58 #if $minMappingQuality and $minMappingQuality is not None:
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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59 --minMappingQuality $minMappingQuality
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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60 #end if
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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61
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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62 #if $chromosomeSizes:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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63 --chromosomeSizes '$chromosomeSizes'
2
eb0d14cdf8b8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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64 #end if
eb0d14cdf8b8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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65
eb0d14cdf8b8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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66 --threads @THREADS@
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495ae38f6e0d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
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67
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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68 --QCfolder ./QCfolder
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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69 &&
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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70 mv ./QCfolder/* $qc.files_path/
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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71 &&
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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72 mv '$qc.files_path/hicQC.html' '$qc'
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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73 && mv "$qc.files_path"/*.log raw_qc
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74 && mv matrix.$outputFormat matrix
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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75 #if $outBam:
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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76 && samtools sort -@ @THREADS@ -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
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77 #end if
0
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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78 ]]>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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79 </command>
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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80 <inputs>
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9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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81 <!-- can we use multiple=True here with min="2" and max="2" ? -->
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
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82 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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83 <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
9edf8894a22d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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84 <validator type="unspecified_build" />
2
eb0d14cdf8b8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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85 </param>
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86 </repeat>
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87
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88 <expand macro="restrictionCutFile" />
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89 <expand macro="restrictionSequence" />
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90 <expand macro="danglingSequence" />
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91
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92 <param argument="--minDistance" type="integer" optional="true" value="" label="Minimum distance between restriction sites" help="Restriction sites that are closer that this distance are merged into one.
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93 This option only applies if --restrictionCutFile is given." />
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94 <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
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95 which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
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96 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
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97 is too far away from the nearest restriction site." />
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98
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99 <repeat name='binSizes' title='Bin size in bp' min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
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100 Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
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101 <param argument="--binSize" type="integer" optional="true" value="" label="Bin size in bp" />
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102 </repeat>
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104 <expand macro="region" />
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105 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
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106 <param argument="--removeSelfLigation" type="boolean" truevalue="--removeSelfLigation" falsevalue="" label="remove self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are removed. Although this reads do not contribute to any distant contact, they are useful to account for bias in the data" />
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107 <expand macro="minMappingQuality" />
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108 <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." />
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109 <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected
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110 Usually the sizes can be determined from the SAM/BAM input files, however,
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111 for cHi-C or scHi-C it can be that at the start or end no data is present.
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112 Please consider that this option causes that only reads are considered which are on the listed chromosomes.
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113 Use this option to guarantee fixed sizes. An example file is available via UCSC:
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114 http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" />
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115
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116 <param argument='--outBam' type='boolean' truevalue='--outBam' falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam
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117 file containing all valid Hi-C reads can be created
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118 using this option. This bam file could be useful to
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119 inspect the distribution of valid Hi-C reads pairs or
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120 for other downstream analyses, but is not used by any
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121 HiCExplorer tool. Computation will be significantly
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122 longer if this option is set." />
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123
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124 <param name='outputFormat' type='select' label="Output file format">
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125 <option value='h5'>HiCExplorer format</option>
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126 <option value="cool">cool</option>
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127 </param>
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128 </inputs>
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129 <outputs>
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130 <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}">
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131 <filter>outBam</filter>
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132 </data>
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133 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
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134 <change_format>
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135 <when input="outputFormat" value="cool" format="cool" />
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136 </change_format>
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137 </data>
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138 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
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139 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
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140 </outputs>
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141 <tests>
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142 <test expect_num_outputs="4">
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143 <repeat name="samFiles">
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144 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
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145 </repeat>
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146 <repeat name="samFiles">
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147 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
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148 </repeat>
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149 <param name='outputFormat' value='h5' />
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150 <repeat name='binSizes'>
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151 <param name="binSize" value="5000" />
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152 </repeat>
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153 <param name='restrictionCutFile' value='DpnII_10k.bed' />
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154 <param name='restrictionSequence' value='GATC' />
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155 <param name='danglingSequence' value='GATC' />
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156 <param name='outBam' value="True" />
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157 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
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158 <output name="outFileName" ftype="h5">
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159 <assert_contents>
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160 <has_h5_keys keys='intervals,matrix' />
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161 </assert_contents>
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162 </output>
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163 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2' />
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164 </test>
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165 <test expect_num_outputs="4">
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166 <repeat name="samFiles">
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167 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
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168 </repeat>
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169 <repeat name="samFiles">
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170 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
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171 </repeat>
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172 <repeat name='binSizes'>
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173 <param name="binSize" value="5000" />
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174 </repeat>
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175 <param name='restrictionCutFile' value='DpnII_10k.bed' />
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176 <param name='restrictionSequence' value='GATC' />
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177 <param name='danglingSequence' value='GATC' />
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178 <param name='outputFormat' value='cool' />
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179 <param name='outBam' value="True" />
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180 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
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181 <output name="outFileName" ftype="cool">
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182 <assert_contents>
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183 <has_h5_keys keys='bins,chroms,indexes,pixels' />
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184 </assert_contents>
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185 </output>
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186 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2' />
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187 </test>
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188 </tests>
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189 <help><![CDATA[
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190
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191 Creation of the contact matrix
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192 ===============================
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193
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194
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195 **hicBuildMatrix** creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files
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196 corresponding to the first and second mates of the paired-end Hi-C reads mapped on the reference genome.
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197 The sam and bam files should not be sorted by position. There are two main options to create the Hi-C contact matrix,
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198 either by fixed bin size (eg. 10000 bp) or by bins of variable length following restriction enzyme sites location in the genome (restriction enzyme resolution).
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199 **hicBuildMatrix** generates a quality control output that can be used to analyze the quality of the Hi-C reads to assess if the experiment and sequencing were successful.
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200
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201 _________________
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202
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203
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204 Usage
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205 -----
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206
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207
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208 This tool must be used on paired sam / bam files produced with a program that supports local alignment (e.g. Bowtie2) where both PE reads are mapped using the --local option.
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209
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210 _________________
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211
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212
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213 Output
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214 ------
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215
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216 **hicBuildMatrix** creates multiple outputs:
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217
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218 - The contact matrix used by HiCExplorer for all downstream analyses.
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219 - A bam file with the accepted alignments, which can be useful to inspect the distribution of valid Hi-C reads pairs, notably around restriction enzyme sites or for other downstream analyses. This file is not used by any HiCExplorer tools.
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220 - A quality control report to assess if the Hi-C protocol and library contrusction were successful.
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221
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222 Example plot
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223 ++++++++++++
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224
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225 .. image:: hicPlotMatrix.png
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226 :width: 50%
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227
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228 Contact matrix of *Drosophila melanogaster* embryos built with **hicBuildMatrix** and visualized using ``hicPlotMatrix``. Hi-C matrix bins were merged to a 25 kb bin size before plotting using ``hicMergeMatrixBins``.
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229
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230
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231
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232
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233 Quality report
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234 ++++++++++++++
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235
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236 A quality report is produced alongside the contact matrix.
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237
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238 .. image:: $PATH_TO_IMAGES/hicQC.png
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239 :width: 40%
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240
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241 Several plots, that are described in details below, are comprised inside this report.
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242
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243 .. image:: $PATH_TO_IMAGES/hicQC_pairs_sequenced.png
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244 :width: 40%
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245
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246 On the plot above, we can see how many reads were sequenced per sample (pairs considered), how many reads were mappable, unique and of high quality and how many reads passed all quality controls and are thus useful for further analysis (pairs used). All quality controls used for read filtering are explained below.
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247
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248 .. image:: $PATH_TO_IMAGES/hicQC_unmappable_and_non_unique.png
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249 :width: 40%
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251 The figure above contains the fraction of reads with respect to the total number of reads that did not map, that have a low quality score or that didn't map uniquely to the genome. In our example we can see that Sample 3 has the highest fraction of pairs used. We explain the differences between the three samples on the plot below.
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253 .. image:: $PATH_TO_IMAGES/hicQC_pairs_discarded.png
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254 :width: 40%
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256 This figure contains the fraction of read pairs (with respect to mappable and unique reads) that were discarded when building the Hi-C matrix. You can find the description of each category below:
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258 - **Dangling ends:** reads that start with the restriction site and constitute reads that were digested but not ligated. Sample 1 in our example has a high fraction of dangling ends (and thus a low proportion of pairs used). Reasons for this can be inefficient ligation or insufficient removal of danging ends during samples preparation.
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259
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260 - **Duplicated pairs:** reads that have the same sequence due to PCR amplification. For example, Sample 2 was amplified too much and thus has a very high fraction of duplicated pairs.
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262 - **Same fragment:** read mates facing inward, separated by up to 800bp that do not have a restriction enzyme site in between. These read pairs are not valid Hi-C pairs and are thus discarded from further analyses.
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264 - **Self circle:** read pairs within 25kb with 'outward' read orientation.
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266 - **Self ligation:** read pairs with a restriction site in between that are within 800bp.
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268 .. image:: $PATH_TO_IMAGES/hicQC_distance.png
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269 :width: 40%
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271 The figure above contains the fraction of read pairs (with respect to mappable reads) that compose inter chromosomal, short range (< 20kb) or long range contacts. Inter chromosomal reads of a wild-type sample are expected to be low. Trans-chromosomal contacts can be primarily considered as random ligation events. These would be expected to contribute to technical noise that may obscure some of the finer features in the Hi-C datasets (Nagano *et al.* 2015, Comparison of Hi-C results using in-solution versus in-nucleus ligation, doi: https://doi.org/10.1186/s13059-015-0753-7). As such, a high fraction of inter chromosomal reads is an indicator of low sample quality, but it can also be associated to cell cycle changes (Nagano *et al.* 2018, Cell-cycle dynamics of chromosomal organisation at single-cell resolution, doi: https://doi.org/10.1038/nature23001).
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273 Short range and long range contacts proportions can be associated to how the fixation is performed during Hi-C sample preparation. These two proportions also directly impact the Hi-C corrected counts versus genomic distance plots generated by hicPlotDistVsCounts.
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275 .. image:: $PATH_TO_IMAGES/hicQC_read_orientation.png
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276 :width: 40%
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278 The last figure shows the fractions of inward, outward, left or right read pairs (with respect to mappable reads). Deviations from an equal distribution indicates problems during sample preparation.
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280 _________________
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282 | For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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284 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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285 ]]> </help>
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286 <expand macro="citations" />
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287 </tool>