Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 0:70cdd1d37637 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
author bgruening
date Sun, 09 Oct 2016 17:35:10 -0400
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children 8116270ba934
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-1:000000000000 0:70cdd1d37637
1 <tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Plots a HiC matrix heatmap</description>
3 <macros>
4 <token name="@BINARY@">hicPlotMatrix</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>
9 <![CDATA[
10 ln -s '$matrix' input_matrix.npz.h5 &&
11
12 @BINARY@
13
14 --matrix input_matrix.npz.h5
15
16 #if $title and $title is not None:
17 --title '$title'
18 #end if
19
20 #if $scoreName and $scoreName is not None:
21 --scoreName '$scoreName'
22 #end if
23
24 #if $outFileName and $outFileName is not None:
25 --outFileName plot.png
26 #end if
27
28 $perChromosome
29 $clearMaskedBins
30
31
32 --whatToShow $whatToShow.whatToShow_select
33
34
35 ## special: --chromosomeOrder is optional, but if given needs at least one argument
36 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
37 #if chroms
38 --chromosomeOrder "$chroms"
39 #end if
40
41 #if $region and $region is not None:
42 --region $region
43 #end if
44
45 #if $region2 and $region2 is not None:
46 --region2 $region2
47 #end if
48 $log1p
49 $log
50
51 #if $colorMap and $colorMap is not None:
52 --colorMap $colorMap
53 #end if
54
55 #if $vMin and $vMin is not None:
56 --vMin $vMin
57 #end if
58
59 #if $vMax and $vMax is not None:
60 --vMax $vMax
61 #end if
62
63 #if $whatToShow.whatToShow_select != 'heatmap':
64 --zMax $zMax
65 #end if
66
67 ]]>
68 </command>
69 <inputs>
70 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
71 <param argument="--title" type="text" optional="true" label="Plot title"/>
72 <param argument="--scoreName" type="text" optional="true" label="Score name"/>
73 <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
74 label="Plot per chromosome"
75 help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
76 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
77 label="Remove masked bins from the matrix" />
78
79 <conditional name="whatToShow">
80 <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
81 <option value="both" selected="true">Show both</option>
82 <option value="heatmap">Only heatmap</option>
83 <option value="3D">Only 3D</option>
84 </param>
85 <when value="both">
86 <expand macro="zMax" />
87 </when>
88 <when value="3D">
89 <expand macro="zMax" />
90 </when>
91 <when value="heatmap"/>
92 </conditional>
93
94 <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):" help="This option overrides --region and --region2">
95 <param name="chromosome" type="text" />
96 </repeat>
97
98 <param argument="--region" type="text" label="Plot only this region"
99 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
100 <param argument="--region2" type="text" label="If given then only the region defined by --region and --region2 is given. The format is the same as --region1"/>
101 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
102 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/>
103
104 <expand macro="colormap" />
105
106 <param argument="--vMin" type="float" optional="true" label="vMin"/>
107 <param argument="--vMax" type="float" optional="true" label="vMax"/>
108 <param argument="--zMax" type="float" optional="true" label="zMax" help="For 3D plots"/>
109
110 </inputs>
111 <outputs>
112 <data name="outFileName" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
113 </outputs>
114 <tests>
115 <test>
116 <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
117 <param name="whatToShow_select" value="heatmap"/>
118 <output name="outFileName" file="hicPlotMatrix_result1.png" ftype="png" compare="sim_size"/>
119 </test>
120 </tests>
121 <help><![CDATA[
122
123 **What it does**
124
125 Plots a HiC matrix heatmap.
126
127 ]]></help>
128 <expand macro="citations" />
129 </tool>
130