Mercurial > repos > bgruening > hicexplorer_hicaggregatecontacts

annotate hicAggregateContacts.xml @ 9:1b25346775db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 06:24:30 -0400
parents ce16a538ab46
children ee370ade24cd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
1
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
2 <tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
3 <description>allow plotting of aggregated Hi-C contacts between regions specified in a file</description>
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
4 <macros>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
5 <token name="@BINARY@">hicAggregateContacts</token>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
6 <import>macros.xml</import>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
7 </macros>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
8 <expand macro="requirements" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
10 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
11 @BINARY@
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
12 --matrix 'matrix.$matrix_h5_cooler.ext'
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
13 --BED $BED
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
14 #if $BED2:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
15 --BED2 $BED2
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
16 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
17
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
18 --range '$range_min:$range_max'
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
19
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
20 --numberOfBins '$numberOfBins'
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
21
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
22 --transform $transform
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
23 --avgType $avgType
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
24
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
25 #if $outputs and 'PrefixMatrix' in $outputs:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
26 --outFilePrefixMatrix 'matrix_values'
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
27 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
28
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
29 #if $outputs and 'ClusterContactPositions' in $outputs:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
30 --outFilePrefixClusterContactPositions 'contact_positions'
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
31 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
32
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
33 #if $outputs and 'HeatmapFile' in $outputs:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
34 --diagnosticHeatmapFile 'heatmap'
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
35 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
36
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
37 #if $clustering:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
38 $clustering
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
39 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
40 $clusterOnDiagonal
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
41
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
42 #if $chromosomes:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
43 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
44 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
45
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
46 #if $plotType:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
47 --plotType $plotType
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
48 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
49
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
50 #if $colormap:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
51 --colorMap $colormap
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
52 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
53
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
54 #if $vMin:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
55 --vMin $vMin
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
56 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
57
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
58 #if $vMax:
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
59 --vMax $vMax
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
60 #end if
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
61
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
62 --outFileName plot.$image_file_format
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
63 && mv plot.$image_file_format plot
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
64
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
65 ]]>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
66 </command>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
67 <inputs>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
68 <expand macro='matrix_h5_cooler_macro' />
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
69 <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted"/>
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
70 <param argument="--BED2" type="data" format="bed" optional="true"
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
71 label="Interactions between regions in first and second BED file are plotted"/>
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
72
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
73 <expand macro='range' />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
74
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
75 <repeat name="chromosomes" title="List of chromosomes to plot" min="0">
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
76 <param name="chromosome" type="text" label="chromosome (one per field)">
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
77 <validator type="empty_field" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
78 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
79 </repeat>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
80
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
81 <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix"
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
82 help="The bed regions will be centered between -half number of bins
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
83 and +half number of bins indicated." />
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
84
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
85 <param argument="--transform" type="select" label="Type of transformation for the matrix"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
86 help="If total counts are selected, then the sub-matrix values
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
87 are divided by the total counts for normalization. If
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
88 z-score or obs/exp are selected, then H-C matrix is
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
89 converted into a z-score or observed / expected matrix.">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
90 <option value="none" selected="true">none</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
91 <option value="total-counts">total-counts</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
92 <option value="z-score">z-score</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
93 <option value="obs/exp">obs/exp</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
94 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
95
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
96 <param argument="--avgType" type="select" label="Type of average to compute final matrix">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
97 <option value="median" selected="true">median</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
98 <option value="mean">mean</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
99 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
100
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
101 <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
102 help="When this option is set, then the matrix is split into
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
103 clusters using the hierarchical clustering algorithm,
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
104 using 'ward linkage'. hclust could be very slow if
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
105 you have >1000 submatrices per chromosome. In those
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
106 cases, you might prefer kmeans.">
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
107 <option value="--kmeans">kmeans</option>
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
108 <option value="--hclust">hclust (#clusters per chromosome)</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
109 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
110
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
111 <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue=""
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
112 label="Perform clustering on the submatrix diagonal"
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
113 help="Clustering is by default carried out on the whole
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
114 submatrices. If this parameter is given, the
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
115 clustering is only carried out based on the submatrix
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
116 diagonal (representing values at the same distance to each other)." />
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
117
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
118 <param argument="--plotType" type="select" optional="true" label="Plot type">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
119 <option value="2d">2D</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
120 <option value="3d">3D</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
121 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
122 <expand macro="colormap" />
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
123 <param argument="--vMin" type="float" optional="true" label="vMin"
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
124 help= "Minimum value of the plotted score." />
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
125
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
126 <param argument="--vMax" type="float" optional="true" label="vMax"
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
127 help= "Maximum value of the plotted score." />
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
128
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
129 <param name="image_file_format" type="select" label="Image output format">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
130 <option value="png" selected="True">png</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
131 <option value="svg">svg</option>
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
132 <option value="pdf">pdf</option>
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
133
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
134 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
135
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
136 <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
137 <option value="PrefixMatrix">Save values underlying the final matrix</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
138 <option value="ClusterContactPositions">Save the position of the contacts</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
139 <option value="HeatmapFile">Heatmap file per chromosome</option>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
140 </param>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
141
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
142 </inputs>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
143 <outputs>
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
144 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
145 <change_format>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
146 <when input="image_file_format" value="svg" format="svg" />
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
147 <when input="image_file_format" value="pdf" format="pdf" />
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
148
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
149 </change_format>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
150 </data>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
151 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
152 <discover_datasets pattern="matrix_values_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
153 </collection>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
154 <collection name="contact_positions" type="list" label="${tool.name} on ${on_string}: Matrix values">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
155 <discover_datasets pattern="contact_positions_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
156 </collection>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
157 <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Matrix values">
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
158 <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
159 </collection>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
160 </outputs>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
161 <tests>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
162 <test>
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
163 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool"/>
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
164 <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed"/>
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
165 <param name="numberOfBins" value="30" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
166 <param name="range_max" value="900000" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
167 <param name="range_min" value="50000" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
168 <param name="image_file_format" value="png" />
5
ce16a538ab46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
bgruening
parents: 2
diff changeset
169 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/>
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
170 </test>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
171 </tests>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
172 <help><![CDATA[
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
173 Aggregation of Hi-C contacts
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
174 ============================
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
175
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
176 **hicAggregateContacts** allows plotting of aggregated Hi-C sub-matrices of a specified list of positions. Positions of interest can for example be binding sites of a specific protein that were determined by ChIP-seq or genetic elements as transcription start sites of active genes.
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
177
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
178 _________________
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
179
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
180 Usage
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
181 -----
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
182
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
183 This tool must be used on Hi-C matrices corrected by ``hicCorrectMatrix``. One should also consider bigger bins than restriction enzyme resolution bins using ``hicMergeMatrixBins``.
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
184
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
185 _________________
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
186
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
187 Optional parameters
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
188 -------------------
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
189
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
190 Optional data output can be selected:
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
191
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
192 - **Save values underlying the final matrix:** if this option is given, then the values underlying the final matrix will be saved to tab-delimited tables (one per chromosome) using the indicated prefix, for example TSS_to_TSS_chrX.tab. If clustering is performed, then the values are saved including the cluster_id a in TSS_to_TSS_chrX_cluster_1.tab
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
193
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
194 - **Save the position of the contacts:** if this option is given, then the position of the contacts is saved as (chrom1, start1, end1, chrom2, start2, end2) where chrom_n, start_n, end_n correspond to the pair of positions used to compute the submatrix. The data is saved per chromosome and per cluster separately (one file each).
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
195
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
196 - **Heatmap file per chromosome:** if given, a heatmap file (per chromosome) is saved. Each row in the heatmap contains the diagonal of each of the submatrices centered on the bed file. This file is useful to get an idea of the values that are used for the aggregate matrix and to determine the fraction of submatrices that are aggregated that may have an enrichment at the center.
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
197
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
198 _________________
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
199
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
200 Output
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
201 ------
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
202
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
203 **hicAggregateContacts** outputs a plot of aggregated contacts.
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
204
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
205 Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosophila melanogaster* Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
206
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
207 .. image:: $PATH_TO_IMAGES/hicAggregateContacts.png
2
2abdd761461b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 1
diff changeset
208 :width: 80 %
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
209
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
210 This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
211
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
212 _________________
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
213
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
214 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
215
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
216 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
1
ec59bf4c3d06 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 0
diff changeset
217 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
0
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
218 ]]></help>
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
219 <expand macro="citations" />
ccd1d3013827 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
220 </tool>