Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 5:c3703afea1b1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:21:50 -0500
parents fd5e51d2b558
children f93a78bc045e
comparison
equal deleted inserted replaced
4:fd5e51d2b558 5:c3703afea1b1
1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Plots a HiC matrix heatmap</description> 2 <description>Plots a HiC 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" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$matrix' input_matrix.h5 && 9
10 10 #if str($pca_conditional.pca_type) == 'bedgraph':
11 ln -s $pca_conditional.pca_bedgraph pca.bedgraph &&
12 #set $pca = '--pca pca.bedgraph'
13 #elif str($pca_conditional.pca_type) == 'bigwig':
14 ln -s $pca_conditional.pca_bigwig pca.bw &&
15 #set $pca = '--pca pca.bw'
16 #elif str($pca_conditional.pca_type) == '':
17 #set $pca = ''
18 #end if
19
11 @BINARY@ 20 @BINARY@
12 21
13 --matrix input_matrix.h5 22 --matrix '$matrix_h5_cooler'
14 23
15 #if $title and $title is not None: 24 #if $title and $title is not None:
16 --title '$title' 25 --title '$title'
17 #end if 26 #end if
18 27
19 #if $scoreName and $scoreName is not None: 28 #if $scoreName and $scoreName is not None:
20 --scoreName '$scoreName' 29 --scoreName '$scoreName'
21 #end if 30 #end if
22 31
23
24 --outFileName plot.$image_file_format 32 --outFileName plot.$image_file_format
25 33
26 $perChromosome 34 $perChromosome
27 $clearMaskedBins 35 $clearMaskedBins
28
29 --whatToShow heatmap
30
31 36
32 ## special: --chromosomeOrder is optional, but if given needs at least one argument 37 ## special: --chromosomeOrder is optional, but if given needs at least one argument
33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) 38 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
34 #if chroms: 39 #if chroms:
35 --chromosomeOrder '$chroms' 40 --chromosomeOrder '$chroms'
55 60
56 #if $vMax: 61 #if $vMax:
57 --vMax $vMax 62 --vMax $vMax
58 #end if 63 #end if
59 64
65 $pca
66
60 && mv plot.$image_file_format plot 67 && mv plot.$image_file_format plot
61 ]]> 68 ]]>
62 </command> 69 </command>
63 <inputs> 70 <inputs>
64 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/> 71 <expand macro='matrix_h5_cooler_macro' />
72
65 <param argument="--title" type="text" optional="true" label="Plot title"/> 73 <param argument="--title" type="text" optional="true" label="Plot title"/>
66 <param argument="--scoreName" type="text" optional="true" label="Score name"/> 74 <param argument="--scoreName" type="text" optional="true" label="Score name"/>
67 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false" 75 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
68 label="Plot per chromosome" 76 label="Plot per chromosome"
69 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" /> 77 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
86 94
87 <expand macro="colormap" /> 95 <expand macro="colormap" />
88 96
89 <param argument="--vMin" type="float" optional="true" label="vMin"/> 97 <param argument="--vMin" type="float" optional="true" label="vMin"/>
90 <param argument="--vMax" type="float" optional="true" label="vMax"/> 98 <param argument="--vMax" type="float" optional="true" label="vMax"/>
99
100 <conditional name="pca_conditional">
101 <param name='pca_type' label='Datatype of eigenvector file' type='select'>
102 <option value='' selected="true"></option>
103 <option value='bedgraph'>bedgraph</option>
104 <option value='bigwig'>bigwig</option>
105 </param>
106 <when value='' />
107 <when value='bedgraph'>
108 <param name='pca_bedgraph' type="data" format="bedgraph"
109 label="Eigenvector file"/>
110 </when>
111 <when value='bigwig'>
112 <param name='pca_bigwig' type="data" format="bigwig"
113 label="Eigenvector file"/>
114 </when>
115 </conditional>
91 <param name="image_file_format" type="select" label="Image output format"> 116 <param name="image_file_format" type="select" label="Image output format">
92 <option value="png" selected="True">png</option> 117 <option value="png" selected="True">png</option>
93 <option value="svg">svg</option> 118 <option value="svg">svg</option>
94 </param> 119 </param>
95 </inputs> 120 </inputs>
100 </change_format> 125 </change_format>
101 </data> 126 </data>
102 </outputs> 127 </outputs>
103 <tests> 128 <tests>
104 <test> 129 <test>
105 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/> 130 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
131 <conditional name="pca_conditional">
132 <param name="pca_type" value=''/>
133 </conditional>
106 <param name="region" value="chrX:3000000-3500000"/> 134 <param name="region" value="chrX:3000000-3500000"/>
107 <param name="region2" value="chrX:3100000-3600000"/> 135 <param name="region2" value="chrX:3100000-3600000"/>
108 <param name="log1p" value="True"/> 136 <param name="log1p" value="True"/>
109 <param name="clearMaskedBins" value="True"/> 137 <param name="clearMaskedBins" value="True"/>
110 <!-- <param name="whatToShow_select" value="heatmap"/> -->
111 <param name="image_file_format" value="png" /> 138 <param name="image_file_format" value="png" />
112 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/> 139 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
140 </test>
141 <test>
142 <param name="matrix_h5_cooler" value="Li_et_al_2015.cool"/>
143 <conditional name="pca_conditional">
144 <param name="pca_type" value=''/>
145 </conditional>
146 <param name="region" value="X:3000000-3500000"/>
147 <param name="image_file_format" value="png" />
148 <output name="outFileName" file="Li_chrX30-35_cool.png" ftype="png" compare="sim_size"/>
149 </test>
150 <test>
151 <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
152 <param name="perChromosome" value="True"/>
153 <conditional name="pca_conditional">
154 <param name="pca_type" value='bedgraph'/>
155 <param name="pca_bedgraph" value="pca1.bedgraph"/>
156 </conditional>
157 <param name='colormap' value='hot'/>
158 <param name="image_file_format" value="svg" />
159 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
160 </test>
161 <test>
162 <param name="matrix_h5_cooler" value="pearson_small_50kb.h5"/>
163 <param name="perChromosome" value="True"/>
164 <conditional name="pca_conditional">
165 <param name="pca_type" value='bigwig'/>
166 <param name="pca_bigwig" value="pca1.bw"/>
167 </conditional>
168 <param name='colormap' value='hot'/>
169
170 <param name="image_file_format" value="svg" />
171 <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
113 </test> 172 </test>
114 </tests> 173 </tests>
115 <help><![CDATA[ 174 <help><![CDATA[
116 Contact matrix plot 175 Contact matrix plot
117 ======================= 176 =======================
118 177
119 ``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. 178 ``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.
120 179 Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
121 .. Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
122 180
123 Input 181 Input
124 ----- 182 -----
125 183
126 Parameters 184 Parameters
127 __________ 185 __________
128 - the contact matrix 186 - the contact matrix: h5 or cool file format.
129 - A title for the plot 187 - A title for the plot
130 - Score name 188 - Score name
131 - per chromosome 189 - per chromosome
132 - The chromosomes to include in the plot. 190 - The chromosomes to include in the plot.
133 - What to show: 191 - What to show:
134 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used. 192 - The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
135 - log / log1p of the values: It is recommended to use log1p. 193 - log / log1p of the values: It is recommended to use log1p.
136 - Colormaps_ for the heatmap. 194 - Colormaps_ for the heatmap.
137 - vMin / vMax 195 - vMin / vMax
138 196 - principal component: a bedgraph or bigwig file containing eigenvector information
139 .. - principal component: a bedgraph file
140 197
141 Output 198 Output
142 ------ 199 ------
143 200
144 The contact matrix plotted for chromosome 1. 201 The contact matrix plotted for chromosome 1.
145 202
146 .. image:: SRR027956.svg 203 .. image:: SRR027956.svg
147 :width: 70% 204 :width: 60%
148 205
149 206
150 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>`_. 207 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>`_.
151 208
152 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png 209 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png