annotate hicPlotDistVsCounts.xml @ 10:d7a84a789c83 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
author iuc
date Sat, 09 Jun 2018 15:34:40 -0400
parents c886ddb8e122
children 34dc1acfcc62
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
8
62803bb47880 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
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
3 <macros>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
4 <token name="@BINARY@">hicPlotDistVsCounts</token>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
5 <import>macros.xml</import>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
6 </macros>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
7 <expand macro="requirements" />
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
9 #import re
f768ce54ee2a 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=[]
f768ce54ee2a 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=[]
f768ce54ee2a 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):
f768ce54ee2a 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($m.element_identifier))
5
819bd2c44d4a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents: 4
diff changeset
14 ln -f -s '${m}' '${identifier}_${counter}' &&
819bd2c44d4a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents: 4
diff changeset
15 #silent $matrices_path.append("'%s_%s'" % ($identifier, $counter))
1
f768ce54ee2a 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))
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
17 #end for
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
18
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
19 @BINARY@
1
f768ce54ee2a 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($matrices_path)#
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
21 --labels #echo " ".join($matrices_labels)#
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
22 $skipDiagonal
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
23 --plotFile plot.png
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
24 #if $plotsize:
f768ce54ee2a 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
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
26 #end if
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
27 --maxdepth $maxdepth
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
28 $perchr
f768ce54ee2a 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
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
30 #if $chromosomeExclude:
2
9b664f43a90e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
31 --chromosomeExclude '$chroms'
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
32 #end if
10
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
33
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
34 #if $outFileData_Boolean:
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
35 $outFileData_Boolean ./outFileData
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
36 #end if
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
37 ]]>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
38 </command>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
39 <inputs>
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
40 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices"/>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
41
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
42 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts"
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
43 help="If set, diagonal counts are not included"/>
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
44 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
45 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." />
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
46 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
47 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
48 <param argument="--plotsize" type="text" optional="True" label="Plot size"
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
49 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." />
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
50 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
51 help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
2
9b664f43a90e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
52 <param argument="--chromosomeExclude" type="text" value="" >
9b664f43a90e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
53 <validator type="empty_field" />
9b664f43a90e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
54 </param>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
55 </repeat>
10
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
56 <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM"
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
57 help="A bam file containing all data underlying the plots is saved on this file."/>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
58 </inputs>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
59 <outputs>
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
60 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
10
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
61 <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
62 <filter>outFileData_Boolean</filter>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
63 </data>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
64 </outputs>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
65 <tests>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
66 <test>
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
67 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
68 <param name="skipDiagonal" value="False"/>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
69 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
70 </test>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
71 <test>
10
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
72 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
73 <param name="skipDiagonal" value="False"/>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
74 <param name='outFileData_Boolean' value='True'/>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
75 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
76 <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
77 </test>
d7a84a789c83 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
iuc
parents: 9
diff changeset
78 <test>
1
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
79 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
80 <param name="skipDiagonal" value="False"/>
1
f768ce54ee2a 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
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
82 <repeat name="chromosomeExclude">
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
83 <param name="chromosomeExclude" value="chrUextra"/>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
84 </repeat>
1
f768ce54ee2a 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">
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
86 <param name="chromosomeExclude" value="chrM"/>
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
87 </repeat>
f768ce54ee2a 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">
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
89 <param name="chromosomeExclude" value="chr3LHet"/>
f768ce54ee2a planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 07491a9ed4870989c9a603b27a4b89173832700f
bgruening
parents: 0
diff changeset
90 </repeat>
2
9b664f43a90e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
91 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
92 </test>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
93 </tests>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
94 <help><![CDATA[
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
95 Relation of genomic distance and number of contacts
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
96 ===================================================
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
97
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
98 **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.
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
99
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
100 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
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
101
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
102 When plotting multiple matrices, the denser ones (more coverage) are scaled down to match the sum of the smaller matrix of the comparison.
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
103
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
104 _________________
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
105
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
106 Usage
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
107 -----
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
108
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
109 **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``.
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
110
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
111 _________________
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
112
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
113 Output
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
114 ------
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
115
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
116 This program makes distance vs. Hi-C counts plots. It can use several matrix files to compare
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
117 them. If the ``--perchr`` option is given, each chromosome is plotted independently.
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
118 Below can be found an example output:
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
119
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
120 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts.png
9
c886ddb8e122 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 8
diff changeset
121 :scale: 50 %
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
122
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
123 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.
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
124
9
c886ddb8e122 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 8
diff changeset
125
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
126 On the second graph below, the distance vs. Hi-C contact counts is computed and plotted per chromosome:
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
127
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
128 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
9
c886ddb8e122 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7
iuc
parents: 8
diff changeset
129 :scale: 50 %
8
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
130
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
131 _________________
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
132
62803bb47880 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
iuc
parents: 5
diff changeset
133 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
4
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
134
ed96f2fd7e3f planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
135 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
0
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
136 ]]></help>
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
137 <expand macro="citations" />
6abd5817e0cd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
138 </tool>