Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 1:8116270ba934 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Wed, 29 Mar 2017 17:29:36 -0400
parents 70cdd1d37637
children 7c2c17b2c4a6
comparison
equal deleted inserted replaced
0:70cdd1d37637 1:8116270ba934
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ln -s '$matrix' input_matrix.npz.h5 && 10 ln -s '$matrix' input_matrix.h5 &&
11 11
12 @BINARY@ 12 @BINARY@
13 13
14 --matrix input_matrix.npz.h5 14 --matrix input_matrix.h5
15 15
16 #if $title and $title is not None: 16 #if $title and $title is not None:
17 --title '$title' 17 --title '$title'
18 #end if 18 #end if
19 19
20 #if $scoreName and $scoreName is not None: 20 #if $scoreName and $scoreName is not None:
21 --scoreName '$scoreName' 21 --scoreName '$scoreName'
22 #end if 22 #end if
23 23
24 #if $outFileName and $outFileName is not None: 24
25 --outFileName plot.png 25 --outFileName plot.svg
26 #end if
27 26
28 $perChromosome 27 $perChromosome
29 $clearMaskedBins 28 $clearMaskedBins
30
31 29
32 --whatToShow $whatToShow.whatToShow_select 30 --whatToShow $whatToShow.whatToShow_select
33 31
34 32
35 ## special: --chromosomeOrder is optional, but if given needs at least one argument 33 ## special: --chromosomeOrder is optional, but if given needs at least one argument
36 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) 34 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
37 #if chroms 35 #if chroms
38 --chromosomeOrder "$chroms" 36 --chromosomeOrder '$chroms'
39 #end if 37 #end if
40 38
41 #if $region and $region is not None: 39 #if $region:
42 --region $region 40 --region '$region'
43 #end if 41 #end if
44 42
45 #if $region2 and $region2 is not None: 43 #if $region2:
46 --region2 $region2 44 --region2 '$region2'
47 #end if 45 #end if
48 $log1p 46 $log1p
49 $log 47 $log
50 48
51 #if $colorMap and $colorMap is not None: 49 #if $colormap:
52 --colorMap $colorMap 50 --colorMap $colormap
53 #end if 51 #end if
54 52
55 #if $vMin and $vMin is not None: 53 #if $vMin:
56 --vMin $vMin 54 --vMin $vMin
57 #end if 55 #end if
58 56
59 #if $vMax and $vMax is not None: 57 #if $vMax:
60 --vMax $vMax 58 --vMax $vMax
61 #end if 59 #end if
62 60
63 #if $whatToShow.whatToShow_select != 'heatmap': 61 #if $whatToShow.whatToShow_select != 'heatmap':
64 --zMax $zMax 62 #if $whatToShow.zMax:
63 --zMax $whatToShow.zMax
64 #end if
65 #end if 65 #end if
66 66
67 ]]> 67 ]]>
68 </command> 68 </command>
69 <inputs> 69 <inputs>
76 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false" 76 <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
77 label="Remove masked bins from the matrix" /> 77 label="Remove masked bins from the matrix" />
78 78
79 <conditional name="whatToShow"> 79 <conditional name="whatToShow">
80 <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D"> 80 <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
81 <option value="both" selected="true">Show both</option> 81 <option value="both">Show both</option>
82 <option value="heatmap">Only heatmap</option> 82 <option value="heatmap" selected="true">Only heatmap</option>
83 <option value="3D">Only 3D</option> 83 <option value="3D">Only 3D</option>
84 </param> 84 </param>
85 <when value="both"> 85 <when value="both">
86 <expand macro="zMax" /> 86 <expand macro="zMax" />
87 </when> 87 </when>
89 <expand macro="zMax" /> 89 <expand macro="zMax" />
90 </when> 90 </when>
91 <when value="heatmap"/> 91 <when value="heatmap"/>
92 </conditional> 92 </conditional>
93 93
94 <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):" help="This option overrides --region and --region2"> 94 <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):"
95 help="This option overrides --region and --region2">
95 <param name="chromosome" type="text" /> 96 <param name="chromosome" type="text" />
96 </repeat> 97 </repeat>
97 98
98 <param argument="--region" type="text" label="Plot only this region" 99 <param argument="--region" type="text" optional="True" 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 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="--region2" type="text" optional="True" label="Region two to plot"
102 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
101 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/> 103 <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."/> 104 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/>
103 105
104 <expand macro="colormap" /> 106 <expand macro="colormap" />
105 107
106 <param argument="--vMin" type="float" optional="true" label="vMin"/> 108 <param argument="--vMin" type="float" optional="true" label="vMin"/>
107 <param argument="--vMax" type="float" optional="true" label="vMax"/> 109 <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
110 </inputs> 111 </inputs>
111 <outputs> 112 <outputs>
112 <data name="outFileName" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/> 113 <data name="outFileName" from_work_dir="plot.svg" format="svg" label="${tool.name} on ${on_string}"/>
113 </outputs> 114 </outputs>
114 <tests> 115 <tests>
115 <test> 116 <test>
116 <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/> 117 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/>
118 <param name="region" value="chrX:3000000-3500000"/>
119 <param name="region2" value="chrX:3100000-3600000"/>
120 <param name="log1p" value="True"/>
121 <param name="clearMaskedBins" value="True"/>
117 <param name="whatToShow_select" value="heatmap"/> 122 <param name="whatToShow_select" value="heatmap"/>
118 <output name="outFileName" file="hicPlotMatrix_result1.png" ftype="png" compare="sim_size"/> 123 <output name="outFileName" file="hicPlotMatrix_result1.svg" ftype="svg" compare="sim_size"/>
119 </test> 124 </test>
120 </tests> 125 </tests>
121 <help><![CDATA[ 126 <help><![CDATA[
122 127
123 **What it does** 128 **What it does**