Mercurial > repos > bgruening > hicexplorer_hicfindtads

annotate hicFindTADs.xml @ 14:0ccb1df6bbf0 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 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
author iuc
date Mon, 09 Dec 2019 10:22:44 +0000
parents f3d63e9942f7
children ebf8b65ac7b4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
1 <tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
2 <description>identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin</description>
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
3 <macros>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
4 <token name="@BINARY@">hicFindTADs</token>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
5 <import>macros.xml</import>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
6 </macros>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
10
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
11 #if $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed':
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
12 ln -s '$precomputedZscore_conditional.scoreFile' 'prefix_tad_score.bm' &&
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
13 ln -s '$precomputedZscore_conditional.zscoreMatrix' 'prefix_zscore_matrix.h5' &&
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
14 #end if
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
15 @BINARY@
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
16 --matrix 'matrix.$matrix_h5_cooler.ext'
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
17
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
18 --delta $delta
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
19
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
20 #if $minBoundaryDistance:
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
21 --minBoundaryDistance $minBoundaryDistance
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
22 #end if
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
23
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
24 #if $precomputedZscore_conditional.precomputedZscore_selector == 'scratch':
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
25 --minDepth $precomputedZscore_conditional.minDepth
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
26 --maxDepth $precomputedZscore_conditional.maxDepth
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
27 --step $precomputedZscore_conditional.step
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
28 #elif $precomputedZscore_conditional.precomputedZscore_selector == 'precomputed':
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
29 --TAD_sep_score_prefix prefix
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
30 #end if
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
31 #if $multiple_comparison_conditional.multiple_comparison_selector == 'fdr':
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
32 --correctForMultipleTesting fdr
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
33 --threshold $multiple_comparison_conditional.threshold
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
34 #elif $multiple_comparison_conditional.multiple_comparison_selector == 'bonferroni':
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
35 --correctForMultipleTesting bonferroni
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
36 --threshold $multiple_comparison_conditional.threshold
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
37 #else:
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
38 --multipleComparisons None
1
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
39 #end if
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
40
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
41 --numberOfProcessors @THREADS@
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
42 --outPrefix galaxy_tad_prefix
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
43 #if $chromosomes:
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
44 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
45 #end if
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
46 ]]></command>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
47 <inputs>
6
49899531dd07 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 5
diff changeset
48 <expand macro='matrix_h5_cooler_macro' />
49899531dd07 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 5
diff changeset
49
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
50 <conditional name='precomputedZscore_conditional'>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
51 <param name='precomputedZscore_selector' type="select" label="Compute from scratch or use precomputed data">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
52 <option value='scratch' selected='True'>From scratch</option>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
53 <option value='precomputed'>Precomputed z-score matrix</option>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
54 </param>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
55 <when value='scratch'>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
56
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
57 <param argument="--minDepth" type="integer" value="5000"
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
58 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
59 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
60 <param argument="--maxDepth" type="integer" value="10000"
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
61 label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
62 help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
63 <param argument="--step" type="integer" value="10000"
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
64 label="Step size when moving from minDepth to maxDepth"
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
65 help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
66 until it reaches maxDepth. For example, selecting step=10,000, minDepth=20,000
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
67 and maxDepth=150,000 will compute TAD-scores for window sizes:
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
68 20,000, 30,000, 40,000, 70,000 and 100,000"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
69 </when>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
70 <when value='precomputed'>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
71 <param name="scoreFile" type="data" format='bedgraph' label="Precomputed TAD score file (bm)"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
72 <param name="zscoreMatrix" type="data" format='h5' label="Precomputed z-score matrix"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
73 </when>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
74 </conditional>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
75
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
76 <conditional name="multiple_comparison_conditional">
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
77 <param name="multiple_comparison_selector" type="select" label="Multiple Testing Corrections" >
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
78 <option value="fdr" selected="True">False discovery rate</option>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
79 <option value="bonferroni">Bonferroni correction</option>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
80 <option value="None">No correction</option>
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
81 </param>
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
82 <when value="fdr">
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
83 <param name="threshold" type="float" value="0.01" label="q-value" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
84 </when>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
85 <when value="bonferroni">
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
86 <param name="threshold" type="float" value="0.01" label="p-value" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
87 </when>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
88 <when value="None" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
89 </conditional>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
90 <param argument="--delta" type="float" value="0.001" optional="True"
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
91 label="Minimum threshold of the difference between the TAD-separation score of a putative boundary and the mean of the TAD-sep. score of surrounding bins."
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
92 help="The delta value reduces spurious boundaries that are shallow, which usually
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
93 occur at the center of large TADs when the TAD-sep. score is flat. Higher
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
94 delta threshold values produce more conservative boundary estimations. By
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
95 default, multiple delta thresholds are saved for the following delta
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
96 values: 0.001, 0.01, 0.03, 0.05, 0.1. Other single or multiple values
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
97 can be given."/>
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
98
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
99 <param argument="--minBoundaryDistance" type="integer" value="" optional="True"
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
100 label="Minimum distance between boundaries (in bp)."
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
101 help="This parameter can be used to reduce spurious boundaries caused by noise. "/>
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
102 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
103 <param name="chromosome" type="text" label='chromosome (one per field)'>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
104 <validator type="empty_field" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
105 </param>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
106 </repeat>
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
107 </inputs>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
108 <outputs>
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
109
1
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
110 <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed"
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
111 label="${tool.name} on ${on_string}: Boundary positions" />
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
112
1
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
113 <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph"
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
114 label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores" />
1
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
115 <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
116 label="${tool.name} on ${on_string}: TAD domains" />
1
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
117 <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
118 format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" />
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
119
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
120 <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm"
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
121 format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file" >
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
122 <filter>precomputedZscore_conditional.precomputedZscore_selector == 'scratch'</filter>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
123
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
124 </data>
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
125
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
126 <data name="matrix_output" from_work_dir="galaxy_tad_prefix_zscore_matrix.h5"
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
127 format="h5" label="${tool.name} on ${on_string}: Z-score matrix in h5">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
128 <filter>precomputedZscore_conditional.precomputedZscore_selector == 'scratch'</filter>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
129 </data>
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
130 </outputs>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
131 <tests>
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
132 <test>
6
49899531dd07 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 5
diff changeset
133 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
134 <conditional name="precomputedZscore_conditional">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
135 <param name="precomputedZscore_selector" value="scratch"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
136 <param name="minDepth" value="15000"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
137 <param name="maxDepth" value="30000"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
138 <param name="step" value="15000"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
139 </conditional>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
140
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
141 <param name="minBoundaryDistance" value="5000" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
142 <conditional name="multiple_comparison_conditional">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
143 <param name="multiple_comparison_selector" value="fdr"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
144 <param name="threshold" value="0.8" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
145 </conditional>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
146 <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" compare="sim_size" delta="35000" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
147 <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
148 <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
149 <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
150 <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
151 <output name="matrix_output" ftype="h5">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
152 <assert_contents>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
153 <has_h5_keys keys='intervals,matrix'/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
154 </assert_contents>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
155 </output>
6
49899531dd07 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 5
diff changeset
156
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
157 </test>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
158 <test>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
159 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
160 <conditional name="precomputedZscore_conditional">
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
161 <param name="precomputedZscore_selector" value="precomputed"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
162 <param name="scoreFile" value="find_TADs/multiFDR_tad_score.bm" />
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
163 <param name="zscoreMatrix" value="find_TADs/multiFDR_zscore_matrix.h5"/>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
164 </conditional>
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
165 <param name="minBoundaryDistance" value="5000" />
3
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
166 <conditional name="multiple_comparison_conditional">
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
167 <param name="multiple_comparison_selector" value="fdr"/>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
168 <param name="threshold" value="0.1" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
169 </conditional>
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
170 <output name="boundaries" file="find_TADs/multiFDR_boundaries.bed" ftype="bed" compare="sim_size" delta="35000" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
171 <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
172 <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" />
0b4f8cec3441 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
173 <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" />
1
138b5060bc48 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents: 0
diff changeset
174 </test>
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
175 </tests>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
176 <help><![CDATA[
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
177 Calculate Topologic Associated Domains
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
178 ======================================
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
179
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
180 Toplogical domains (TADs) are large mainly self-interacting domains. Chromatin interactions occur with higher frequency within a TAD as between TADs. More information_.
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
181
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
182 _________________
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
183
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
184 Usage
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
185 -----
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
186
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
187 This tool must be used on unmerged matrices (restiction enzyme resolution) produced by ``hicBuildMatrix`` and corrected by ``hicCorrectMatrix``.
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
188
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
189 _________________
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
190
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
191 Computation details
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
192 -------------------
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
193
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
194 **hicFindTADs** computes the TAD regions in two steps: in a first step it computes a TAD-separation score based on a z-score matrix for all bins. The z-score is defined as:
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
195
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
196 “The absolute value of z represents the distance between the raw score and the population mean in
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
197 units of the standard deviation. z is negative when the raw score is below the mean, positive when above.”
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
198 [Source_].
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
199
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
200 .. image:: $PATH_TO_IMAGES/z-score.svg
6
49899531dd07 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
iuc
parents: 5
diff changeset
201 :width: 100
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
202
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
203 `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
204
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
205 In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_.
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
206
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
207 _________________
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
208
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
209 Output
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
210 ------
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
211
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
212 **hicFindTADs** produces multiple outputs:
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
213
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
214 - TAD boundaries positions as a BED file and TAD separation score.
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
215 - TAD boundaries positions with delta, p-value and TAD separation score as GFF.
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
216 - TAD domains as a BED file.
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
217 - TAD seperation score as bigwig (bw), bedgraph and numpy array (npz) format. These files can be used to plot the so-called TAD insulation score or TAD separation score along the genome or at specific regions. This score is much more reliable across samples than the number of TADs or the TADs width that can vary depending on the sequencing depth because of the lack of information at certain bins, and depending on the parameters used with this tool.
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
218 - Matrix with multi-scale TAD scores as a bed-matrix (bm) file that can be plotted inside ``pyGenomeTracks`` to nicely display TAD insulation score alongside Hi-C heatmap and other datasets.
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
219 - Z-score matrix in h5 format that is useful to quickly test the --thresholdComparisons, --delta and --correctForMultipleTesting parameters by using the --TAD_sep_score_prefix option pointing to this zscore_matrix.h5 file (will be added in a future update).
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
220
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
221 _________________
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
222
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
223 Usage hints
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
224 -----------
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
225
14
0ccb1df6bbf0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
iuc
parents: 9
diff changeset
226 It is mandatory to test multiple parameters of TAD calling with **hicFindTADs** before making conclusions about the number of TADs in a given sample or before comparing TAD calling between multiple conditions. In order to compare numerous TAD calling parameters at once, it is recommended to use ``pyGenomeTracks``, below you can find a plot where multiple TAD calling parameters are displayed for *Drosophila melanogaster* embryos:
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
227
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
228 .. image:: $PATH_TO_IMAGES/hicFindTADs_TAD_calling_comparison.png
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
229 :width: 65 %
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
230
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
231 We can see that the fourth set of **hicFindTADs** parameters with a threshold of 0.001 gives the best results in terms of TAD calling compared to the corrected Hi-C counts distribution and compared to the enrichment of H3K36me3, which is known to be enriched at TAD boundaries in *Drosophila melanogaster*.
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
232
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
233 _________________
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
234
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
235 For more information about HiCExplorer please consider our documentation on readthedocs.io_
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
236
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
237 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
9
f3d63e9942f7 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 6
diff changeset
238 .. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score
5
4b2096acb3ab planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 3
diff changeset
239 .. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_
0
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
240 ]]></help>
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
241 <expand macro="citations" />
40f067ea70e2 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
242 </tool>