Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix
annotate hicBuildMatrix.xml @ 26:a7ab0e43ca99 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2024 17:12:45 +0000 |
| parents | 37530b4c6fe4 |
| children |
| rev | line source |
|---|---|
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26
a7ab0e43ca99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
iuc
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1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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10
ee5a82a286ed
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents:
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2 <description>create a contact matrix</description> |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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3 <macros> |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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4 <token name="@BINARY@">hicBuildMatrix</token> |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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5 <import>macros.xml</import> |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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6 </macros> |
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26
a7ab0e43ca99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
iuc
parents:
25
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7 <expand macro="requirements"/> |
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3
41d4044e1dfe
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
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8 <command detect_errors="exit_code"><![CDATA[ |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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9 |
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1
8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 mkdir ./QCfolder && |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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11 mkdir '$qc.files_path' && |
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1a38e937b5ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
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12 @BINARY@ |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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13 --samFiles |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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14 #for $repeat in $samFiles: |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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15 '${repeat.samFile}' |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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16 #end for |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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17 |
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22
c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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18 --restrictionCutFile '$restrictionCutFile' |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
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19 |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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20 #if $restrictionSequence: |
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25
37530b4c6fe4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
iuc
parents:
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21 --restrictionSequence $restrictionSequence |
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22
c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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22 #end if |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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23 #if $danglingSequence: |
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25
37530b4c6fe4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
iuc
parents:
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24 --danglingSequence $danglingSequence |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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25 #end if |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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26 #if $minDistance: |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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27 --minDistance $minDistance |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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28 #end if |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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29 #if $maxLibraryInsertSize: |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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30 --maxLibraryInsertSize $maxLibraryInsertSize |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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31 #end if |
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24
f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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32 |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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33 #if $binSizes: |
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18
aefb1d4c85ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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34 --binSize |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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35 #for $repeat in $binSizes |
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16
1a38e937b5ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents:
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36 '${repeat.binSize}' |
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1a38e937b5ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
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37 #end for |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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38 #end if |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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39 |
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24
f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
diff
changeset
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40 #if $chromosomeSizes: |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
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41 --chromosomeSizes '$chromosomeSizes' |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
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42 #end if |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
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43 #if $dbKey: |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
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44 --genomeAssembly '$dbKey' |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
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45 #else |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
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46 --genomeAssembly '$samFiles[0].samFile.metadata.dbkey' |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
22
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47 #end if |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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48 |
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1
8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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49 #if $region: |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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50 --region '$region' |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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51 #end if |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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52 |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents:
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53 --outFileName 'matrix.$outputFormat' |
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10
ee5a82a286ed
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
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54 |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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55 #if $outBam: |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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56 $outBam ./unsorted.bam |
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10
ee5a82a286ed
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
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57 #end if |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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58 |
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3
41d4044e1dfe
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
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59 $keepSelfCircles |
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f75705bee191
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
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60 $keepSelfLigation |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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61 $skipDuplicationCheck |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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62 |
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1
8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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63 #if $minMappingQuality and $minMappingQuality is not None: |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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64 --minMappingQuality $minMappingQuality |
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611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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65 #end if |
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1
8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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66 |
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3
41d4044e1dfe
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
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67 --threads @THREADS@ |
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10
ee5a82a286ed
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
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68 |
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1
8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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69 --QCfolder ./QCfolder |
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0
611b0f02e109
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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70 && |
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1
8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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71 mv ./QCfolder/* $qc.files_path/ |
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8ffb4beeabcf
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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72 && |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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73 mv '$qc.files_path/hicQC.html' '$qc' |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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74 && mv "$qc.files_path"/*.log raw_qc |
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8
5fd877e2296b
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
parents:
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75 && mv matrix.$outputFormat matrix |
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22
c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents:
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76 #if $outBam: |
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c8f355e10161
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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77 && samtools sort -@ @THREADS@ -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam |
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78 #end if |
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79 ]]> |
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80 </command> |
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81 <inputs> |
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82 <!-- can we use multiple=True here with min="2" and max="2" ? --> |
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83 <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."> |
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84 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"> |
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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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103 |
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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="--keepSelfLigation" type="boolean" truevalue="--keepSelfLigation" falsevalue="" label="Keep self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are kept. 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 <param name="dbKey" type="text" optional="true" label="Use this dbkey for your history genome" |
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116 help="You can set the reference genome in your history as metadata. In case you have not you can specify it here." /> |
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117 |
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118 <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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119 file containing all valid Hi-C reads can be created |
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120 using this option. This bam file could be useful to |
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121 inspect the distribution of valid Hi-C reads pairs or |
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122 for other downstream analyses, but is not used by any |
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123 HiCExplorer tool. Computation will be significantly |
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124 longer if this option is set." /> |
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125 |
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126 <param name="outputFormat" type="select" label="Output file format"> |
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127 <option value="h5">HiCExplorer format</option> |
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128 <option value="cool">cool</option> |
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129 </param> |
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130 </inputs> |
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131 <outputs> |
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132 <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"> |
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133 <filter>outBam</filter> |
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134 </data> |
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135 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> |
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136 <change_format> |
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137 <when input="outputFormat" value="cool" format="cool" /> |
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138 </change_format> |
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139 </data> |
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140 <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> |
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141 <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" /> |
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142 </outputs> |
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143 <tests> |
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144 <test expect_num_outputs="4"> |
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145 <repeat name="samFiles"> |
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146 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> |
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147 </repeat> |
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148 <repeat name="samFiles"> |
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149 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> |
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150 </repeat> |
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151 <param name="outputFormat" value="h5" /> |
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152 <repeat name="binSizes"> |
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153 <param name="binSize" value="5000" /> |
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154 </repeat> |
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155 <param name="restrictionCutFile" value="DpnII_10k.bed" /> |
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156 <param name="restrictionSequence" value="GATC" /> |
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157 <param name="danglingSequence" value="GATC" /> |
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158 <param name="outBam" value="True" /> |
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159 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" /> |
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160 <output name="outFileName" ftype="h5"> |
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161 <assert_contents> |
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162 <has_h5_keys keys="intervals,matrix" /> |
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163 </assert_contents> |
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164 </output> |
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165 <output name="raw_qc" file="raw_qc_report" compare="diff" lines_diff="2" /> |
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166 </test> |
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167 <test expect_num_outputs="4"> |
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168 <repeat name="samFiles"> |
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169 <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> |
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170 </repeat> |
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171 <repeat name="samFiles"> |
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172 <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> |
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173 </repeat> |
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174 <repeat name="binSizes"> |
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175 <param name="binSize" value="5000" /> |
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176 </repeat> |
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177 <param name="restrictionCutFile" value="DpnII_10k.bed" /> |
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178 <param name="restrictionSequence" value="GATC" /> |
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179 <param name="danglingSequence" value="GATC" /> |
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180 <param name="outputFormat" value="cool" /> |
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181 <param name="outBam" value="True" /> |
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182 <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" /> |
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183 <output name="outFileName" ftype="cool"> |
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184 <assert_contents> |
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185 <has_h5_keys keys="bins,chroms,indexes,pixels" /> |
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186 </assert_contents> |
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187 </output> |
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188 <output name="raw_qc" file="raw_qc_report" compare="diff" lines_diff="2" /> |
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189 </test> |
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190 </tests> |
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191 <help><![CDATA[ |
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192 |
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193 Creation of the contact matrix |
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194 =============================== |
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195 |
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196 |
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197 **hicBuildMatrix** creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files |
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198 corresponding to the first and second mates of the paired-end Hi-C reads mapped on the reference genome. |
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199 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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200 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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201 **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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202 |
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203 _________________ |
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204 |
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205 |
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206 Usage |
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207 ----- |
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208 |
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209 |
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210 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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211 |
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212 _________________ |
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213 |
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214 |
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215 Output |
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216 ------ |
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217 |
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218 **hicBuildMatrix** creates multiple outputs: |
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219 |
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220 - The contact matrix used by HiCExplorer for all downstream analyses. |
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221 - 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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222 - A quality control report to assess if the Hi-C protocol and library contrusction were successful. |
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224 Example plot |
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225 ++++++++++++ |
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226 |
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227 .. image:: hicPlotMatrix.png |
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228 :width: 50% |
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229 |
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230 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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234 |
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235 Quality report |
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236 ++++++++++++++ |
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237 |
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238 A quality report is produced alongside the contact matrix. |
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239 |
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240 .. image:: $PATH_TO_IMAGES/hicQC.png |
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241 :width: 40% |
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242 |
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243 Several plots, that are described in details below, are comprised inside this report. |
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244 |
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245 .. image:: $PATH_TO_IMAGES/hicQC_pairs_sequenced.png |
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246 :width: 40% |
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247 |
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248 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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249 |
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250 .. image:: $PATH_TO_IMAGES/hicQC_unmappable_and_non_unique.png |
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251 :width: 40% |
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252 |
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253 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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254 |
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255 .. image:: $PATH_TO_IMAGES/hicQC_pairs_discarded.png |
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256 :width: 40% |
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257 |
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258 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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259 |
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260 - **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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261 |
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262 - **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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263 |
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264 - **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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265 |
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266 - **Self circle:** read pairs within 25kb with 'outward' read orientation. |
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267 |
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268 - **Self ligation:** read pairs with a restriction site in between that are within 800bp. |
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269 |
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270 .. image:: $PATH_TO_IMAGES/hicQC_distance.png |
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271 :width: 40% |
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272 |
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273 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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274 |
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275 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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276 |
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277 .. image:: $PATH_TO_IMAGES/hicQC_read_orientation.png |
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278 :width: 40% |
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279 |
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280 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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281 |
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282 _________________ |
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283 |
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284 | For more information about HiCExplorer please consider our documentation on readthedocs.io_. |
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285 |
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286 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
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287 ]]> </help> |
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288 <expand macro="citations" /> |
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289 </tool> |