Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 19:7babd8a46fe0 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 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:24:48 +0000
parents b553d14a7845
children 9939786dd9c9
comparison
equal deleted inserted replaced
18:5308ca68ef3d 19:7babd8a46fe0
1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>plot a Hi-C contact 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>
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 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext && 16 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
17 @BINARY@ 17 @BINARY@
18
19
20 --matrix 'matrix.$matrix_h5_cooler.ext' 18 --matrix 'matrix.$matrix_h5_cooler.ext'
21 19
22 #if $title and $title is not None: 20 #if $title and $title is not None:
23 --title '$title' 21 --title '$title'
24 #end if 22 #end if
89 87
90 #if $rotationY: 88 #if $rotationY:
91 --rotationY $rotationY 89 --rotationY $rotationY
92 #end if 90 #end if
93 91
92 #if $increaseFigureWidth:
93 --increaseFigureWidth $increaseFigureWidth
94 #end if
95
96 #if $increaseFigureHeight:
97 --increaseFigureHeight $increaseFigureHeight
98 #end if
99
94 #if $loops: 100 #if $loops:
95 --loops '$loops' 101 --loops '$loops'
96 #end if 102 #end if
97 && mv plot.$image_file_format plot 103 && mv plot.$image_file_format plot
98 ]]> 104 ]]>
99 </command> 105 </command>
100 <inputs> 106 <inputs>
101 <expand macro='matrix_h5_cooler_macro' /> 107 <expand macro='matrix_h5_cooler_macro' />
102 108
103 <param argument="--title" type="text" optional="true" label="Plot title"/> 109 <param argument="--title" type="text" optional="true" label="Plot title">
104 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend."/> 110 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
105 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" 111 </param>
106 label="Plot per chromosome" 112 <param argument="--scoreName" type="text" optional="true" label="Score name" help="The label for the heatmap legend.">
107 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" /> 113 <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
108 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" 114 </param>
109 label="Remove masked bins from the matrix" /> 115 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" label="Plot per chromosome" help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
110 116 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" label="Remove masked bins from the matrix" />
111 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):" 117
112 help="This option overrides --region and --region2" > 118 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):" help="This option overrides --region and --region2">
113 <param name="chromosome" type="text" > 119 <param name="chromosome" type="text">
114 <validator type="empty_field" /> 120 <validator type="empty_field" />
115 </param> 121 </param>
116 </repeat> 122 </repeat>
117 123
118 <param argument="--region" type="text" optional="True" label="Plot only this region" 124 <param argument="--region" type="text" optional="True" label="Plot only this region" help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given">
119 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> 125 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">value.replace(':', '').replace('-', '').isalnum()</validator>
120 <param argument="--region2" type="text" optional="True" label="Region two to plot" 126 </param>
121 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/> 127 <param argument="--region2" type="text" optional="True" label="Region two to plot" help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region">
122 <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."/> 128 <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">value.replace(':', '').replace('-', '').isalnum()</validator>
123 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/> 129 </param>
124 <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis."/> 130 <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." />
125 <param argument="--rotationX" type="integer" optional="true" label="Rotate x-labels by degree" help="Rotation in degrees for the labels of x-axis."/> 131 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))" />
126 <param argument="--rotationY" type="integer" optional="true" label="Rotate y-labels by degree" help="Rotation in degrees for the labels of y-axis."/> 132 <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis." />
127 133 <param argument="--rotationX" type="integer" optional="true" label="Rotate x-labels by degree" help="Rotation in degrees for the labels of x-axis." />
134 <param argument="--rotationY" type="integer" optional="true" label="Rotate y-labels by degree" help="Rotation in degrees for the labels of y-axis." />
135 <param argument="--increaseFigureWidth" type="float" value='0.5' optional="true" label="Increase figure width size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." />
136 <param argument="--increaseFigureHeight" type="float" value='0.5' optional="true" label="Increase figure height size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." />
128 <expand macro="colormap" /> 137 <expand macro="colormap" />
129 138
130 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/> 139 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score." />
131 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/> 140 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score." />
132 141
133 <conditional name="pca_conditional"> 142 <conditional name="pca_conditional">
134 <param name='pca_type' label='Datatype of eigenvector file' type='select'> 143 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
135 <option value='' selected="true"></option> 144 <option value='' selected="true"></option>
136 <option value='bigwig'>bigwig</option> 145 <option value='bigwig'>bigwig</option>
137 </param> 146 </param>
138 <when value='' /> 147 <when value='' />
139 <when value='bigwig'> 148 <when value='bigwig'>
140 <param name='pca_bigwig' type="data" format="bigwig" 149 <param name='pca_bigwig' type="data" format="bigwig" label="Eigenvector file" />
141 label="Eigenvector file"/> 150 <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score." />
142 <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score."/> 151 <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score." />
143 <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score."/>
144 <param name='flipBigwigSign' type='boolean' optional="true" truevalue='--flipBigwigSign' falsevalue='' label='Flip the sign of the bigwig values' /> 152 <param name='flipBigwigSign' type='boolean' optional="true" truevalue='--flipBigwigSign' falsevalue='' label='Flip the sign of the bigwig values' />
145 <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor."/> 153 <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor." />
146 <param name='bigwigAdditionalVerticalAxis' type='boolean' optional="true" truevalue='--bigwigAdditionalVerticalAxis' falsevalue='' label='Plot an additional vertical axis.' /> 154 <param name='bigwigAdditionalVerticalAxis' type='boolean' optional="true" truevalue='--bigwigAdditionalVerticalAxis' falsevalue='' label='Plot an additional vertical axis.' />
147
148
149 </when> 155 </when>
150 </conditional> 156 </conditional>
151 <param name='loops' type="data" format="interval" optional='True' label="Add detected loops"/> 157 <param name='loops' type="data" format="interval" optional='True' label="Add detected loops" />
152 <param name="image_file_format" type="select" label="Image output format"> 158 <param name="image_file_format" type="select" label="Image output format">
153 <option value="png" selected="True">png</option> 159 <option value="png" selected="True">png</option>
154 <option value="svg">svg</option> 160 <option value="svg">svg</option>
155 <option value="pdf">pdf</option> 161 <option value="pdf">pdf</option>
156 162 </param>
157 </param> 163 <expand macro="dpi" />
158 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
159 </inputs> 164 </inputs>
160 <outputs> 165 <outputs>
161 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot"> 166 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
162 <change_format> 167 <change_format>
163 <when input="image_file_format" value="svg" format="svg" /> 168 <when input="image_file_format" value="svg" format="svg" />
165 </change_format> 170 </change_format>
166 </data> 171 </data>
167 </outputs> 172 </outputs>
168 <tests> 173 <tests>
169 <test> 174 <test>
170 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 175 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
171 <conditional name="pca_conditional"> 176 <conditional name="pca_conditional">
172 <param name="pca_type" value=''/> 177 <param name="pca_type" value='' />
173 </conditional> 178 </conditional>
174 <param name="region" value="chr2L:3000000-3500000"/> 179 <param name="region" value="chr2L:3000000-3500000" />
175 <param name="region2" value="chr2L:3100000-3600000"/> 180 <param name="region2" value="chr2L:3100000-3600000" />
176 <param name="log1p" value="True"/> 181 <param name="log1p" value="True" />
177 <param name="clearMaskedBins" value="True"/> 182 <param name="clearMaskedBins" value="True" />
178 <param name="image_file_format" value="png" /> 183 <param name="image_file_format" value="png" />
179 <param name="dpi" value="10" /> 184 <param name="dpi" value="10" />
180 185
181 <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size"/> 186 <output name="outFileName" file="hicPlotMatrix/plot1.png" ftype="png" compare="sim_size" />
182 </test> 187 </test>
183 <test> 188 <test>
184 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> 189 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
185 <param name="region" value="chr2L:3000000-3500000"/> 190 <param name="region" value="chr2L:3000000-3500000" />
186
187 <conditional name="pca_conditional"> 191 <conditional name="pca_conditional">
188 <param name="pca_type" value=''/> 192 <param name="pca_type" value='' />
189 </conditional> 193 </conditional>
190 <param name="image_file_format" value="pdf" /> 194 <param name="image_file_format" value="pdf" />
191 <param name="dpi" value="10" /> 195 <param name="dpi" value="10" />
192 196 <output name="outFileName" file="hicPlotMatrix/plot2.pdf" ftype="pdf" compare="sim_size" />
193 <output name="outFileName" file="hicPlotMatrix/plot2.pdf" ftype="pdf" compare="sim_size"/>
194 </test> 197 </test>
195 <test> 198 <test>
196 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> 199 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
197 <conditional name="pca_conditional"> 200 <conditional name="pca_conditional">
198 <param name="pca_type" value='bigwig'/> 201 <param name="pca_type" value='bigwig' />
199 <param name="pca_bigwig" value="hicPCA/pca1_test1.bw"/> 202 <param name="pca_bigwig" value="hicPCA/pca1_test1.bw" />
200 <param name='vMinBigwig' value='10'/> 203 <param name='vMinBigwig' value='10' />
201 <param name='vMaxBigwig' value='20'/> 204 <param name='vMaxBigwig' value='20' />
202 <param name='scaleFactorBigwig' value='2000'/> 205 <param name='scaleFactorBigwig' value='2000' />
203 <param name='flipBigwigSign' value='True'/> 206 <param name='flipBigwigSign' value='True' />
204 </conditional> 207 </conditional>
205 <param name='colormap' value='hot'/> 208 <param name='colormap' value='hot' />
206 <param name="region" value="chr2L:3000000-3500000"/> 209 <param name="region" value="chr2L:3000000-3500000" />
207 <param name="dpi" value="10" /> 210 <param name="dpi" value="10" />
208 211
209 <param name="image_file_format" value="svg" /> 212 <param name="image_file_format" value="svg" />
210 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/> 213 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" />
211 </test> 214 </test>
212
213 </tests> 215 </tests>
214 <help><![CDATA[ 216 <help><![CDATA[
217
215 Contact matrix plot 218 Contact matrix plot
216 ======================= 219 =======================
217 220
218 **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. 221 **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.
219 Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments. 222 Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments.
246 249
247 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 250 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
248 251
249 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 252 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
250 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html 253 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
251 ]]></help> 254 ]]> </help>
252 <expand macro="citations" /> 255 <expand macro="citations" />
253 </tool> 256 </tool>