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comparison hicAggregateContacts.xml @ 1:ec59bf4c3d06 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 03:32:37 -0400
parents ccd1d3013827
children 2abdd761461b
comparison
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0:ccd1d3013827 1:ec59bf4c3d06
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1 <tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 2 <tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Takes a list of positions in the hic-matrix and makes a pooled image</description> 3 <description>allow plotting of aggregated Hi-C contacts between regions specified in a file</description>
3 <macros> 4 <macros>
4 <token name="@BINARY@">hicAggregateContacts</token> 5 <token name="@BINARY@">hicAggregateContacts</token>
5 <import>macros.xml</import> 6 <import>macros.xml</import>
6 </macros> 7 </macros>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
62 63
63 ]]> 64 ]]>
64 </command> 65 </command>
65 <inputs> 66 <inputs>
66 <expand macro='matrix_h5_cooler_macro' /> 67 <expand macro='matrix_h5_cooler_macro' />
67 <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted."/> 68 <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted"/>
68 <param argument="--BED2" type="data" format="bed" optional="true" 69 <param argument="--BED2" type="data" format="bed" optional="true"
69 label="Interactions between regions in first and second BED file are plotted."/> 70 label="Interactions between regions in first and second BED file are plotted"/>
70 71
71 <expand macro='range' /> 72 <expand macro='range' />
72 73
73 <repeat name="chromosomes" title="List of chromosomes to plot" min="0"> 74 <repeat name="chromosomes" title="List of chromosomes to plot" min="0">
74 <param name="chromosome" type="text"> 75 <param name="chromosome" type="text" label="chromosome (one per field)">
75 <validator type="empty_field" /> 76 <validator type="empty_field" />
76 </param> 77 </param>
77 </repeat> 78 </repeat>
78 79
79 <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix" 80 <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix"
80 help=" The bed regions will be centered between - half number of bins 81 help="The bed regions will be centered between -half number of bins
81 and the other half number of bins." /> 82 and +half number of bins indicated." />
82 83
83 <param argument="--transform" type="select" label="Type of transformation for the matrix" 84 <param argument="--transform" type="select" label="Type of transformation for the matrix"
84 help="If total counts are selected, then the sub-matrix values 85 help="If total counts are selected, then the sub-matrix values
85 are divided by the total counts for normalization. If 86 are divided by the total counts for normalization. If
86 z-score or obs/exp are selected, then H-C matrix is 87 z-score or obs/exp are selected, then H-C matrix is
97 </param> 98 </param>
98 99
99 <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome" 100 <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome"
100 help="When this option is set, then the matrix is split into 101 help="When this option is set, then the matrix is split into
101 clusters using the hierarchical clustering algorithm, 102 clusters using the hierarchical clustering algorithm,
102 using 'ward linkage'. --hclust could be very slow if 103 using 'ward linkage'. hclust could be very slow if
103 you have >1000 submatrices per chromosome. In those 104 you have >1000 submatrices per chromosome. In those
104 cases, you might prefer --kmeans"> 105 cases, you might prefer kmeans.">
105 <option value="--kmeans">kmenas</option> 106 <option value="--kmeans">kmeans</option>
106 <option value="--hclust">hclust (#clusters per chromosome)</option> 107 <option value="--hclust">hclust (#clusters per chromosome)</option>
107 </param> 108 </param>
108 109
109 <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue="" 110 <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue=""
110 label="Perform clustering on the submatrix diagonal" 111 label="Perform clustering on the submatrix diagonal"
111 help="Clustering is by default carried out on the whole 112 help="Clustering is by default carried out on the whole
112 submatrices. If this parameter is given, the 113 submatrices. If this parameter is given, the
113 clustering is only carried out based on the submatrix 114 clustering is only carried out based on the submatrix
114 diagonal (representing values at the same distance to each other)" /> 115 diagonal (representing values at the same distance to each other)." />
115 116
116 <param argument="--plotType" type="select" optional="true" label="Plot type"> 117 <param argument="--plotType" type="select" optional="true" label="Plot type">
117 <option value="2d">2D</option> 118 <option value="2d">2D</option>
118 <option value="3d">3D</option> 119 <option value="3d">3D</option>
119 </param> 120 </param>
120 <expand macro="colormap" /> 121 <expand macro="colormap" />
121 <param argument="--vMin" type="float" optional="true" label="vMin"/> 122 <param argument="--vMin" type="float" optional="true" label="vMin"
122 <param argument="--vMax" type="float" optional="true" label="vMax"/> 123 help= "Minimum value of the plotted score." />
124
125 <param argument="--vMax" type="float" optional="true" label="vMax"
126 help= "Maximum value of the plotted score." />
123 127
124 <param name="image_file_format" type="select" label="Image output format"> 128 <param name="image_file_format" type="select" label="Image output format">
125 <option value="png" selected="True">png</option> 129 <option value="png" selected="True">png</option>
126 <option value="svg">svg</option> 130 <option value="svg">svg</option>
127 </param> 131 </param>
132 <option value="HeatmapFile">Heatmap file per chromosome</option> 136 <option value="HeatmapFile">Heatmap file per chromosome</option>
133 </param> 137 </param>
134 138
135 </inputs> 139 </inputs>
136 <outputs> 140 <outputs>
137 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}"> 141 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
138 <change_format> 142 <change_format>
139 <when input="image_file_format" value="svg" format="svg" /> 143 <when input="image_file_format" value="svg" format="svg" />
140 </change_format> 144 </change_format>
141 </data> 145 </data>
142 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values"> 146 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
159 <param name="image_file_format" value="png" /> 163 <param name="image_file_format" value="png" />
160 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" /> 164 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
161 </test> 165 </test>
162 </tests> 166 </tests>
163 <help><![CDATA[ 167 <help><![CDATA[
164 --outFilePrefixMatrix OUTFILEPREFIXMATRIX 168 Aggregation of Hi-C contacts
165 If this option is given, then the values underlying 169 ============================
166 the final matrix will be saved to tab-delimited tables 170
167 (one per chromosome) using the indicated prefix, for 171 **hicAggregateContacts** allows plotting of aggregated Hi-C sub-matrices of a specified list of positions. Positions of interest can for example be binding sites of a specific protein that were determined by ChIP-seq or genetic elements as transcription start sites of active genes.
168 example TSS_to_TSS_chrX.tab. If clustering is 172
169 performed, then the values are saved including the 173 _________________
170 cluster_id a in TSS_to_TSS_chrX_cluster_1.tab 174
171 --outFilePrefixClusterContactPositions OUTFILEPREFIXCLUSTERCONTACTPOSITIONS 175 Usage
172 If this option is given, then the position of the 176 -----
173 contacts is saved as (chrom1, start1, end1, chrom2, 177
174 start2, end2) where chrom_n, start_n, end_n correspond 178 This tool must be used on Hi-C matrices corrected by ``hicCorrectMatrix``. One should also consider bigger bins than restriction enzyme resolution bins using ``hicMergeMatrixBins``.
175 to the pair ofpositions used to compute the submatrix. 179
176 The data is saved per chromosome and per cluster 180 _________________
177 separatedly (one file each) 181
178 --diagnosticHeatmapFile DIAGNOSTICHEATMAPFILE 182 Optional parameters
179 If given, a heatmap file (per chromosome) is saved. 183 -------------------
180 Each row in the heatmap contains thediagonal of each 184
181 of the submatrices centered on the bed file. This file 185 Optional data output can be selected:
182 is useful to get an idea of the values that are used 186
183 for the aggregate matrix and to determine the fraction 187 - **Save values underlying the final matrix:** if this option is given, then the values underlying the final matrix will be saved to tab-delimited tables (one per chromosome) using the indicated prefix, for example TSS_to_TSS_chrX.tab. If clustering is performed, then the values are saved including the cluster_id a in TSS_to_TSS_chrX_cluster_1.tab
184 of sub-matrices that are aggregated that may have an 188
185 enrichment at the center. 189 - **Save the position of the contacts:** if this option is given, then the position of the contacts is saved as (chrom1, start1, end1, chrom2, start2, end2) where chrom_n, start_n, end_n correspond to the pair of positions used to compute the submatrix. The data is saved per chromosome and per cluster separately (one file each).
186 190
187 191 - **Heatmap file per chromosome:** if given, a heatmap file (per chromosome) is saved. Each row in the heatmap contains the diagonal of each of the submatrices centered on the bed file. This file is useful to get an idea of the values that are used for the aggregate matrix and to determine the fraction of submatrices that are aggregated that may have an enrichment at the center.
192
193 _________________
194
195 Output
196 ------
197
198 **hicAggregateContacts** outputs a plot of aggregated contacts.
199
200 Below, you can find an example of an aggregate Hi-C matrix obtained from *Drosophila melanogaster* Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.
201
202 .. image:: $PATH_TO_IMAGES/hicAggregateContacts.png
203
204 This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.
205
206 _________________
188 207
189 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 208 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
190 209
191 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 210 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
211 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
192 ]]></help> 212 ]]></help>
193 <expand macro="citations" /> 213 <expand macro="citations" />
194 </tool> 214 </tool>