Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

annotate hicPlotDistVsCounts.xml @ 25:034c35bfe5e9 draft default tip

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 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 17:30:45 +0000
parents a8cd3d005733
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
2 <description>compute distance vs Hi-C counts plot per chromosome</description>
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
3 <macros>
4aa65933bc9b 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@">hicPlotDistVsCounts</token>
4aa65933bc9b 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>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
6 </macros>
4aa65933bc9b 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" />
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
9 #import re
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
10 #set matrices_path=[]
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
11 #set matrices_labels=[]
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
12 #for $counter, $m, in enumerate($matrices):
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
13 #set identifier = re.sub('[^\s\w\-]', '_', str($m.element_identifier))
15
a370923a657f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 14
diff changeset
14 ln -f -s '${m}' '${identifier}_${counter}.$m.ext' &&
a370923a657f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"
iuc
parents: 14
diff changeset
15 #silent $matrices_path.append("'%s_%s.%s'" % ($identifier, $counter, $m.ext))
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
16 #silent $matrices_labels.append("'%s'" % ($identifier))
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
17 #end for
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
18
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
19 @BINARY@
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
20 --matrices #echo " ".join($matrices_path)#
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
21 --labels #echo " ".join($matrices_labels)#
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
22 $skipDiagonal
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
23 --plotFile plot.png
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
24 #if $plotsize:
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
25 --plotsize $plotsize
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
26 #end if
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
27 --maxdepth $maxdepth
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
28 $perchr
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
29 #set chroms = " ".join([ "'%s'" % $var.chromosomeExclude for $var in $chromosomeExclude ])
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
30 #if $chromosomeExclude:
2
3928cf4921b1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
31 --chromosomeExclude '$chroms'
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
32 #end if
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
33 #if $domains:
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
34 --domains '$domains'
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
35 #end if
11
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
36 #if $outFileData_Boolean:
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
37 $outFileData_Boolean ./outFileData
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
38 #end if
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
39 ]]>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
40 </command>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
41 <inputs>
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
42 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices" />
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
43
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
44 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" help="If set, diagonal counts are not included" />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
45 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" help="If more than one Hi-C matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
46 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
47 <param argument="--plotsize" type="text" optional="True" label="Plot size" help="Width and height of the plot (in inches). Default is 6 * number of cols, 4 * number of rows. The maximum number of rows is 4. Example: 6 5.">
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
48 <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
49 </param>
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
50 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
51 <param argument="--chromosomeExclude" type="text" value="">
2
3928cf4921b1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
52 <validator type="empty_field" />
3928cf4921b1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 1
diff changeset
53 </param>
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
54 </repeat>
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
55 <param argument="--domains" type="data" format="bed" optional="True" label="Bed file with domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." />
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
56
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
57 <param name="outFileData_Boolean" type="boolean" truevalue="--outFileData" falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." />
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
58 </inputs>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
59 <outputs>
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
60 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot" />
11
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
61 <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
62 <filter>outFileData_Boolean</filter>
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
63 </data>
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
64 </outputs>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
65 <tests>
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
66 <test expect_num_outputs="1">
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
67 <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
68 <param name="skipDiagonal" value="False" />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
69 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
70 </test>
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
71 <test expect_num_outputs="2">
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
72 <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
73 <param name="skipDiagonal" value="False" />
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
74 <param name="outFileData_Boolean" value="True" />
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
75 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
76 <output name="outFileData" file="distVsCounts.txt" ftype="txt" />
11
4a3ccb7d4fc9 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit fd5d2211338239af6c577d66aeee3bb275c9b15b
iuc
parents: 10
diff changeset
77 </test>
23
a8cd3d005733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
iuc
parents: 21
diff changeset
78 <test expect_num_outputs="1">
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
79 <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5" />
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
80 <param name="skipDiagonal" value="False" />
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
81 <param name="perchr" value="True" />
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
82 <repeat name="chromosomeExclude">
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
83 <param name="chromosomeExclude" value="chrUextra" />
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
84 </repeat>
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
85 <repeat name="chromosomeExclude">
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
86 <param name="chromosomeExclude" value="chrM" />
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
87 </repeat>
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
88 <repeat name="chromosomeExclude">
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
89 <param name="chromosomeExclude" value="chr3LHet" />
1
0ef2a42eca43 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
90 </repeat>
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
91 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" />
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
92 </test>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
93 </tests>
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
94 <help><![CDATA[
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
95
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
96 Relation of genomic distance and number of contacts
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
97 ===================================================
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
98
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
99 **hicPlotDistVsCounts** allows a quick comparison between multiple Hi-C matrices of the Hi-C counts enrichment at different genomic ranges / distances up to whole chromosome. Biological replicates should display the exact same distribution while samples coming from different cell-lines, treated versus untreated samples or mutant versus wild-type samples should display a different distribution at long and/or close range.
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
100
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
101 The results of this tool usually reflect the proportion of long-range and short-range contacts calculated in each sample by ``hicQC`` (which is part of ``hicBuildMatrix``). Local TAD or contact enrichments will not impact the results computed by this tool, ``hicPCA`` is better suited for that purpose.
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
102
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
103 When plotting multiple matrices, the denser ones (more coverage) are scaled down to match the sum of the smaller matrix of the comparison.
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
104
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
105 _________________
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
106
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
107 Usage
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
108 -----
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
109
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
110 **hicPlotDistVsCounts** should be used on corrected matrices with large bins (e.g. at least 30 to 50kb bins), otherwise the curves will be spiky at longer ranges because of the sparness of the contacts, thus the likelyness of the samples will become hard to assess after a certain distance. **hicPlotDistVsCounts** is thus often ran after ``hicMergeMatrixBins`` and ``hicCorrectMatrix``.
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
111
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
112 _________________
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
113
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
114 Output
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
115 ------
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
116
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
117 This program makes distance vs. Hi-C counts plots. It can use several matrix files to compare
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
118 them. If the ``--perchr`` option is given, each chromosome is plotted independently.
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
119 Below can be found an example output:
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
120
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
121 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts.png
10
b6fbf07de5af planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 8
diff changeset
122 :scale: 50 %
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
123
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
124 Here, we see that the samples from the first condition are not so well correlated, but they follow the same tendancies and are distinct from the two samples of the second condition. The later are well correlated and display enriched long-range contacts compared to the first condition samples.
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
125
10
b6fbf07de5af planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 8
diff changeset
126
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
127 On the second graph below, the distance vs. Hi-C contact counts is computed and plotted per chromosome:
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
128
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
129 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
10
b6fbf07de5af planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 8
diff changeset
130 :scale: 50 %
8
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
131
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
132 _________________
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
133
c20b74e7f79c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
134 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
4
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
135
fd133bb2ed84 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
136 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
21
746becb5d022 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
parents: 15
diff changeset
137 ]]> </help>
0
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
138 <expand macro="citations" />
4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
139 </tool>