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comparison hicPlotDistVsCounts.xml @ 8:62803bb47880 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:30:39 -0400
parents 819bd2c44d4a
children c886ddb8e122
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7:ea39c587161f 8:62803bb47880
1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>distance vs HiC counts plot per chromosome</description> 2 <description>compute distance vs Hi-C counts plot per chromosome</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotDistVsCounts</token> 4 <token name="@BINARY@">hicPlotDistVsCounts</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
31 --chromosomeExclude '$chroms' 31 --chromosomeExclude '$chroms'
32 #end if 32 #end if
33 ]]> 33 ]]>
34 </command> 34 </command>
35 <inputs> 35 <inputs>
36 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="HiC normalized (corrected) matrices"/> 36 <param argument="--matrices" type="data" format="h5,cool" multiple="True" label="Hi-C corrected matrices"/>
37 37
38 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" /> 38 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts"
39 help="If set, diagonal counts are not included"/>
39 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome" 40 <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" label="Generate plots per chromosome"
40 help="If more than one HiC matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." /> 41 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." />
41 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth" 42 <param argument="--maxdepth" type="integer" value="3000000" label="Max Depth"
42 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." /> 43 help="Maximum distance from diagonal to use. In other words, distances up to maxDeph are computed." />
43 <param argument="--plotsize" type="text" optional="True" label="Plot size" 44 <param argument="--plotsize" type="text" optional="True" label="Plot size"
44 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 --plotsize 6 5." /> 45 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." />
45 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude" 46 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude"
46 help="This is useful for example to exclude the Y chromosome."> 47 help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
47 <param argument="--chromosomeExclude" type="text" value="" > 48 <param argument="--chromosomeExclude" type="text" value="" >
48 <validator type="empty_field" /> 49 <validator type="empty_field" />
49 </param> 50 </param>
50 </repeat> 51 </repeat>
51
52 </inputs> 52 </inputs>
53 <outputs> 53 <outputs>
54 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/> 54 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
55 </outputs> 55 </outputs>
56 <tests> 56 <tests>
57 <test> 57 <test>
58 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/> 58 <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
59 <param name="skipDiagonal" value="False"/> 59 <param name="skipDiagonal" value="False"/>
75 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/> 75 <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
76 </test> 76 </test>
77 </tests> 77 </tests>
78 <help><![CDATA[ 78 <help><![CDATA[
79 Relation of genomic distance and number of contacts 79 Relation of genomic distance and number of contacts
80 ======================================================== 80 ===================================================
81 81
82 | This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare 82 **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.
83 | them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case
84 | of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
85 | matrices denser matrices are scaled down to match the sum of the smaller matrix.
86 |
87 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
88 83
84 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.
89 85
90 Input 86 When plotting multiple matrices, the denser ones (more coverage) are scaled down to match the sum of the smaller matrix of the comparison.
87
88 _________________
89
90 Usage
91 ----- 91 -----
92 92
93 Parameters 93 **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``.
94 __________ 94
95 - contact matrix 95 _________________
96 - skip diagonal
97 - per chromosome
98 - max depth
99 - plot size
100 - chromosome(s) to exclude
101 96
102 Output 97 Output
103 ------- 98 ------
104 Output if all data in the contact matrix is considered:
105 99
106 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png 100 This program makes distance vs. Hi-C counts plots. It can use several matrix files to compare
107 :width: 70% 101 them. If the ``--perchr`` option is given, each chromosome is plotted independently.
102 Below can be found an example output:
108 103
109 Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome: 104 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts.png
105 :width: 65%
106
107 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.
108
109 On the second graph below, the distance vs. Hi-C contact counts is computed and plotted per chromosome:
110 110
111 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png 111 .. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
112 :width: 80% 112 :width: 80%
113
114 _________________
115
116 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
113 117
114 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 118 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
115 ]]></help> 119 ]]></help>
116 <expand macro="citations" /> 120 <expand macro="citations" />
117 </tool> 121 </tool>
118