Mercurial > repos > bgruening > hicexplorer_hicplotmatrix
comparison hicPlotMatrix.xml @ 4:fd5e51d2b558 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author | iuc |
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date | Sat, 16 Dec 2017 16:30:53 -0500 |
parents | 2c0069f645bc |
children | c3703afea1b1 |
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3:00855c36a2cb | 4:fd5e51d2b558 |
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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 |