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comparison hicPlotMatrix.xml @ 4:fd5e51d2b558 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:30:53 -0500
parents 2c0069f645bc
children c3703afea1b1
comparison
equal deleted inserted replaced
3:00855c36a2cb 4:fd5e51d2b558
1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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>
24 --outFileName plot.$image_file_format 24 --outFileName plot.$image_file_format
25 25
26 $perChromosome 26 $perChromosome
27 $clearMaskedBins 27 $clearMaskedBins
28 28
29 --whatToShow '$whatToShow.whatToShow_select' 29 --whatToShow heatmap
30 30
31 31
32 ## special: --chromosomeOrder is optional, but if given needs at least one argument 32 ## special: --chromosomeOrder is optional, but if given needs at least one argument
33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) 33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
34 #if chroms: 34 #if chroms:
55 55
56 #if $vMax: 56 #if $vMax:
57 --vMax $vMax 57 --vMax $vMax
58 #end if 58 #end if
59 59
60 #if $whatToShow.whatToShow_select != 'heatmap':
61 #if $whatToShow.zMax:
62 --zMax $whatToShow.zMax
63 #end if
64 #end if
65 && mv plot.$image_file_format plot 60 && mv plot.$image_file_format plot
66 ]]> 61 ]]>
67 </command> 62 </command>
68 <inputs> 63 <inputs>
69 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/> 64 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
73 label="Plot per chromosome" 68 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" /> 69 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" 70 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
76 label="Remove masked bins from the matrix" /> 71 label="Remove masked bins from the matrix" />
77 72
78 <conditional name="whatToShow">
79 <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
80 <option value="both">Show both</option>
81 <option value="heatmap" selected="true">Only heatmap</option>
82 <option value="3D">Only 3D</option>
83 </param>
84 <when value="both">
85 <expand macro="zMax" />
86 </when>
87 <when value="3D">
88 <expand macro="zMax" />
89 </when>
90 <when value="heatmap"/>
91 </conditional>
92
93 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):" 73 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
94 help="This option overrides --region and --region2" > 74 help="This option overrides --region and --region2" >
95 <param name="chromosome" type="text" > 75 <param name="chromosome" type="text" >
96 <validator type="empty_field" /> 76 <validator type="empty_field" />
97 </param> 77 </param>
100 <param argument="--region" type="text" optional="True" label="Plot only this region" 80 <param argument="--region" type="text" optional="True" label="Plot only this region"
101 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> 81 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
102 <param argument="--region2" type="text" optional="True" label="Region two to plot" 82 <param argument="--region2" type="text" optional="True" label="Region two to plot"
103 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/> 83 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
104 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/> 84 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
105 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/> 85 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values."/>
106 86
107 <expand macro="colormap" /> 87 <expand macro="colormap" />
108 88
109 <param argument="--vMin" type="float" optional="true" label="vMin"/> 89 <param argument="--vMin" type="float" optional="true" label="vMin"/>
110 <param argument="--vMax" type="float" optional="true" label="vMax"/> 90 <param argument="--vMax" type="float" optional="true" label="vMax"/>
125 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/> 105 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/>
126 <param name="region" value="chrX:3000000-3500000"/> 106 <param name="region" value="chrX:3000000-3500000"/>
127 <param name="region2" value="chrX:3100000-3600000"/> 107 <param name="region2" value="chrX:3100000-3600000"/>
128 <param name="log1p" value="True"/> 108 <param name="log1p" value="True"/>
129 <param name="clearMaskedBins" value="True"/> 109 <param name="clearMaskedBins" value="True"/>
130 <param name="whatToShow_select" value="heatmap"/> 110 <!-- <param name="whatToShow_select" value="heatmap"/> -->
131 <param name="image_file_format" value="png" /> 111 <param name="image_file_format" value="png" />
132 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/> 112 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
133 </test> 113 </test>
134 </tests> 114 </tests>
135 <help><![CDATA[ 115 <help><![CDATA[
116 Contact matrix plot
117 =======================
136 118
137 **What it does** 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.
138 120
139 Plots a Hi-C matrix heatmap. 121 .. Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
140 122
123 Input
124 -----
125
126 Parameters
127 __________
128 - the contact matrix
129 - A title for the plot
130 - Score name
131 - per chromosome
132 - The chromosomes to include in the plot.
133 - 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.
135 - log / log1p of the values: It is recommended to use log1p.
136 - Colormaps_ for the heatmap.
137 - vMin / vMax
138
139 .. - principal component: a bedgraph file
140
141 Output
142 ------
143
144 The contact matrix plotted for chromosome 1.
145
146 .. image:: SRR027956.svg
147 :width: 70%
148
149
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>`_.
151
152 .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
153 :width: 70 %
154
155 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
156
157 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
158 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
141 ]]></help> 159 ]]></help>
142 <expand macro="citations" /> 160 <expand macro="citations" />
143 </tool> 161 </tool>
144 162