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comparison hicPlotMatrix.xml @ 10:ca631354e522 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 03:09:39 -0400
parents 79d10df2108e
children 4053214bebac
comparison
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9:79d10df2108e 10:ca631354e522
1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Plots a HiC matrix heatmap</description> 2 <description>plot a Hi-C contact matrix heatmap</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotMatrix</token> 4 <token name="@BINARY@">hicPlotMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
11 ln -s $pca_conditional.pca_bigwig pca.bw && 11 ln -s $pca_conditional.pca_bigwig pca.bw &&
12 #set $pca = '--bigwig pca.bw' 12 #set $pca = '--bigwig pca.bw'
13 #elif str($pca_conditional.pca_type) == '': 13 #elif str($pca_conditional.pca_type) == '':
14 #set $pca = '' 14 #set $pca = ''
15 #end if 15 #end if
16 16
17 @BINARY@ 17 @BINARY@
18 18
19 --matrix '$matrix_h5_cooler' 19 --matrix '$matrix_h5_cooler'
20 20
21 #if $title and $title is not None: 21 #if $title and $title is not None:
66 </command> 66 </command>
67 <inputs> 67 <inputs>
68 <expand macro='matrix_h5_cooler_macro' /> 68 <expand macro='matrix_h5_cooler_macro' />
69 69
70 <param argument="--title" type="text" optional="true" label="Plot title"/> 70 <param argument="--title" type="text" optional="true" label="Plot title"/>
71 <param argument="--scoreName" type="text" optional="true" label="Score name"/> 71 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/>
72 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" 72 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
73 label="Plot per chromosome" 73 label="Plot per chromosome"
74 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" /> 74 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
75 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" 75 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
76 label="Remove masked bins from the matrix" /> 76 label="Remove masked bins from the matrix" />
84 84
85 <param argument="--region" type="text" optional="True" label="Plot only this region" 85 <param argument="--region" type="text" optional="True" label="Plot only this region"
86 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> 86 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
87 <param argument="--region2" type="text" optional="True" label="Region two to plot" 87 <param argument="--region2" type="text" optional="True" label="Region two to plot"
88 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/> 88 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
89 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/> 89 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
90 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/> 90 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>
91 91
92 <expand macro="colormap" /> 92 <expand macro="colormap" />
93 93
94 <param argument="--vMin" type="float" optional="true" label="vMin"/> 94 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/>
95 <param argument="--vMax" type="float" optional="true" label="vMax"/> 95 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/>
96 96
97 <conditional name="pca_conditional"> 97 <conditional name="pca_conditional">
98 <param name='pca_type' label='Datatype of eigenvector file' type='select'> 98 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
99 <option value='' selected="true"></option> 99 <option value='' selected="true"></option>
100 <option value='bigwig'>bigwig</option> 100 <option value='bigwig'>bigwig</option>
101 </param> 101 </param>
102 <when value='' /> 102 <when value='' />
103 <when value='bigwig'> 103 <when value='bigwig'>
104 <param name='pca_bigwig' type="data" format="bigwig" 104 <param name='pca_bigwig' type="data" format="bigwig"
105 label="Eigenvector file"/> 105 label="Eigenvector file"/>
106 </when> 106 </when>
107 </conditional> 107 </conditional>
108 <param name="image_file_format" type="select" label="Image output format"> 108 <param name="image_file_format" type="select" label="Image output format">
109 <option value="png" selected="True">png</option> 109 <option value="png" selected="True">png</option>
110 <option value="svg">svg</option> 110 <option value="svg">svg</option>
111 </param> 111 </param>
112 </inputs> 112 </inputs>
113 <outputs> 113 <outputs>
114 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}"> 114 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
115 <change_format> 115 <change_format>
116 <when input="image_file_format" value="svg" format="svg" /> 116 <when input="image_file_format" value="svg" format="svg" />
117 </change_format> 117 </change_format>
118 </data> 118 </data>
119 </outputs> 119 </outputs>
156 <conditional name="pca_conditional"> 156 <conditional name="pca_conditional">
157 <param name="pca_type" value='bigwig'/> 157 <param name="pca_type" value='bigwig'/>
158 <param name="pca_bigwig" value="pca1.bw"/> 158 <param name="pca_bigwig" value="pca1.bw"/>
159 </conditional> 159 </conditional>
160 <param name='colormap' value='hot'/> 160 <param name='colormap' value='hot'/>
161 161
162 <param name="image_file_format" value="svg" /> 162 <param name="image_file_format" value="svg" />
163 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/> 163 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
164 </test> 164 </test>
165 </tests> 165 </tests>
166 <help><![CDATA[ 166 <help><![CDATA[
167 Contact matrix plot 167 Contact matrix plot
168 ======================= 168 =======================
169 169
170 ``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other. 170 **hicPlotMatrix** is a visualization tool for Hi-C contact matrices. It supports to plot genome-wide contact matrices, one or multiple chromosomes, a region or two regions against each other.
171 Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments. 171 Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments.
172 172
173 Input 173 _________________
174
175 Usage
174 ----- 176 -----
175 177
176 Parameters 178 This tool can be used on any h5 or cool Hi-C contact matrix. It is noteworthy that for comparisons of 2 matrices or more, they must all have the same or similar number of contacts.
177 __________ 179
178 - the contact matrix: h5 or cool file format. 180 _________________
179 - A title for the plot
180 - Score name
181 - per chromosome
182 - The chromosomes to include in the plot.
183 - What to show:
184 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
185 - log / log1p of the values: It is recommended to use log1p.
186 - Colormaps_ for the heatmap.
187 - vMin / vMax
188 - principal component: a bigwig file containing eigenvector information
189 181
190 Output 182 Output
191 ------ 183 ------
192 184
193 The contact matrix plotted for chromosome 1. 185 **hicPlotMatrix** outputs a heatmap of a contact matrix in either png or svg format, below is an example of such a plot:
194 186
195 .. image:: SRR027956.svg 187 .. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
196 :width: 60% 188 :width: 50%
197 189
198 190 Contact matrix of *Drosophila melanogaster* embryos visualized using **hicPlotMatrix**. Hi-C matrix bins were merged to a 25 kb bin size using ``hicMergeMatrixBins`` and the matrix has then been corrected using ``hicCorrectMatrix`` before plotting.
199 The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, `GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_. 191
192 Another example is available below using Hi-C data published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, (`GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``.
200 193
201 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png 194 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
202 :width: 70 % 195 :width: 70 %
196
197 _________________
203 198
204 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 199 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
205 200
206 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 201 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
207 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html 202 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
208 ]]></help> 203 ]]></help>
209 <expand macro="citations" /> 204 <expand macro="citations" />
210 </tool> 205 </tool>
211