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comparison hicAggregateContacts.xml @ 0:ccd1d3013827 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:37:18 -0500
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children ec59bf4c3d06
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-1:000000000000 0:ccd1d3013827
1 <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 <macros>
4 <token name="@BINARY@">hicAggregateContacts</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@
10 --matrix '$matrix_h5_cooler'
11 --BED $BED
12 #if $BED2:
13 --BED2 $BED2
14 #end if
15
16 --range $range_min:$range_max
17
18 --numberOfBins $numberOfBins
19
20 --transform $transform
21 --avgType $avgType
22
23 #if $outputs and 'PrefixMatrix' in $outputs:
24 --outFilePrefixMatrix 'matrix_values'
25 #end if
26
27 #if $outputs and 'ClusterContactPositions' in $outputs:
28 --outFilePrefixClusterContactPositions 'contact_positions'
29 #end if
30
31 #if $outputs and 'HeatmapFile' in $outputs:
32 --diagnosticHeatmapFile 'heatmap'
33 #end if
34
35 #if $clustering:
36 $clustering
37 #end if
38 $clusterOnDiagonal
39
40 #if $chromosomes:
41 --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
42 #end if
43
44 #if $plotType:
45 --plotType $plotType
46 #end if
47
48 #if $colormap:
49 --colorMap $colormap
50 #end if
51
52 #if $vMin:
53 --vMin $vMin
54 #end if
55
56 #if $vMax:
57 --vMax $vMax
58 #end if
59
60 --outFileName plot.$image_file_format
61 && mv plot.$image_file_format plot
62
63 ]]>
64 </command>
65 <inputs>
66 <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="--BED2" type="data" format="bed" optional="true"
69 label="Interactions between regions in first and second BED file are plotted."/>
70
71 <expand macro='range' />
72
73 <repeat name="chromosomes" title="List of chromosomes to plot" min="0">
74 <param name="chromosome" type="text">
75 <validator type="empty_field" />
76 </param>
77 </repeat>
78
79 <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 and the other half number of bins." />
82
83 <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 are divided by the total counts for normalization. If
86 z-score or obs/exp are selected, then H-C matrix is
87 converted into a z-score or observed / expected matrix.">
88 <option value="none" selected="true">none</option>
89 <option value="total-counts">total-counts</option>
90 <option value="z-score">z-score</option>
91 <option value="obs/exp">obs/exp</option>
92 </param>
93
94 <param argument="--avgType" type="select" label="Type of average to compute final matrix">
95 <option value="median" selected="true">median</option>
96 <option value="mean">mean</option>
97 </param>
98
99 <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 clusters using the hierarchical clustering algorithm,
102 using 'ward linkage'. --hclust could be very slow if
103 you have >1000 submatrices per chromosome. In those
104 cases, you might prefer --kmeans">
105 <option value="--kmeans">kmenas</option>
106 <option value="--hclust">hclust (#clusters per chromosome)</option>
107 </param>
108
109 <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue=""
110 label="Perform clustering on the submatrix diagonal"
111 help="Clustering is by default carried out on the whole
112 submatrices. If this parameter is given, the
113 clustering is only carried out based on the submatrix
114 diagonal (representing values at the same distance to each other)" />
115
116 <param argument="--plotType" type="select" optional="true" label="Plot type">
117 <option value="2d">2D</option>
118 <option value="3d">3D</option>
119 </param>
120 <expand macro="colormap" />
121 <param argument="--vMin" type="float" optional="true" label="vMin"/>
122 <param argument="--vMax" type="float" optional="true" label="vMax"/>
123
124 <param name="image_file_format" type="select" label="Image output format">
125 <option value="png" selected="True">png</option>
126 <option value="svg">svg</option>
127 </param>
128
129 <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
130 <option value="PrefixMatrix">Save values underlying the final matrix</option>
131 <option value="ClusterContactPositions">Save the position of the contacts</option>
132 <option value="HeatmapFile">Heatmap file per chromosome</option>
133 </param>
134
135 </inputs>
136 <outputs>
137 <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}">
138 <change_format>
139 <when input="image_file_format" value="svg" format="svg" />
140 </change_format>
141 </data>
142 <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
143 <discover_datasets pattern="matrix_values_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
144 </collection>
145 <collection name="contact_positions" type="list" label="${tool.name} on ${on_string}: Matrix values">
146 <discover_datasets pattern="contact_positions_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
147 </collection>
148 <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Matrix values">
149 <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
150 </collection>
151 </outputs>
152 <tests>
153 <test>
154 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/>
155 <param name="BED" value="test_regions.bed" ftype="bed"/>
156 <param name="numberOfBins" value="30" />
157 <param name="range_max" value="900000" />
158 <param name="range_min" value="50000" />
159 <param name="image_file_format" value="png" />
160 <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
161 </test>
162 </tests>
163 <help><![CDATA[
164 --outFilePrefixMatrix OUTFILEPREFIXMATRIX
165 If this option is given, then the values underlying
166 the final matrix will be saved to tab-delimited tables
167 (one per chromosome) using the indicated prefix, for
168 example TSS_to_TSS_chrX.tab. If clustering is
169 performed, then the values are saved including the
170 cluster_id a in TSS_to_TSS_chrX_cluster_1.tab
171 --outFilePrefixClusterContactPositions OUTFILEPREFIXCLUSTERCONTACTPOSITIONS
172 If this option is given, then the position of the
173 contacts is saved as (chrom1, start1, end1, chrom2,
174 start2, end2) where chrom_n, start_n, end_n correspond
175 to the pair ofpositions used to compute the submatrix.
176 The data is saved per chromosome and per cluster
177 separatedly (one file each)
178 --diagnosticHeatmapFile DIAGNOSTICHEATMAPFILE
179 If given, a heatmap file (per chromosome) is saved.
180 Each row in the heatmap contains thediagonal of each
181 of the submatrices centered on the bed file. This file
182 is useful to get an idea of the values that are used
183 for the aggregate matrix and to determine the fraction
184 of sub-matrices that are aggregated that may have an
185 enrichment at the center.
186
187
188
189 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
190
191 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
192 ]]></help>
193 <expand macro="citations" />
194 </tool>