Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 2:2c0069f645bc draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:09:46 -0400
parents a9050bffb50c
children fd5e51d2b558
comparison
equal deleted inserted replaced
1:68e57be0d284 2:2c0069f645bc
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>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[
10 ln -s '$matrix' input_matrix.h5 && 9 ln -s '$matrix' input_matrix.h5 &&
11 10
12 @BINARY@ 11 @BINARY@
13 12
14 --matrix input_matrix.h5 13 --matrix input_matrix.h5
20 #if $scoreName and $scoreName is not None: 19 #if $scoreName and $scoreName is not None:
21 --scoreName '$scoreName' 20 --scoreName '$scoreName'
22 #end if 21 #end if
23 22
24 23
25 --outFileName plot.svg 24 --outFileName plot.$image_file_format
26 25
27 $perChromosome 26 $perChromosome
28 $clearMaskedBins 27 $clearMaskedBins
29 28
30 --whatToShow $whatToShow.whatToShow_select 29 --whatToShow '$whatToShow.whatToShow_select'
31 30
32 31
33 ## 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
34 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ]) 33 #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
35 #if chroms 34 #if chroms:
36 --chromosomeOrder '$chroms' 35 --chromosomeOrder '$chroms'
37 #end if 36 #end if
38 37
39 #if $region: 38 #if $region:
40 --region '$region' 39 --region '$region'
61 #if $whatToShow.whatToShow_select != 'heatmap': 60 #if $whatToShow.whatToShow_select != 'heatmap':
62 #if $whatToShow.zMax: 61 #if $whatToShow.zMax:
63 --zMax $whatToShow.zMax 62 --zMax $whatToShow.zMax
64 #end if 63 #end if
65 #end if 64 #end if
66 65 && mv plot.$image_file_format plot
67 ]]> 66 ]]>
68 </command> 67 </command>
69 <inputs> 68 <inputs>
70 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/> 69 <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
71 <param argument="--title" type="text" optional="true" label="Plot title"/> 70 <param argument="--title" type="text" optional="true" label="Plot title"/>
89 <expand macro="zMax" /> 88 <expand macro="zMax" />
90 </when> 89 </when>
91 <when value="heatmap"/> 90 <when value="heatmap"/>
92 </conditional> 91 </conditional>
93 92
94 <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):" 93 <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
95 help="This option overrides --region and --region2"> 94 help="This option overrides --region and --region2" >
96 <param name="chromosome" type="text" /> 95 <param name="chromosome" type="text" >
96 <validator type="empty_field" />
97 </param>
97 </repeat> 98 </repeat>
98 99
99 <param argument="--region" type="text" optional="True" label="Plot only this region" 100 <param argument="--region" type="text" optional="True" label="Plot only this region"
100 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> 101 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
101 <param argument="--region2" type="text" optional="True" label="Region two to plot" 102 <param argument="--region2" type="text" optional="True" label="Region two to plot"
105 106
106 <expand macro="colormap" /> 107 <expand macro="colormap" />
107 108
108 <param argument="--vMin" type="float" optional="true" label="vMin"/> 109 <param argument="--vMin" type="float" optional="true" label="vMin"/>
109 <param argument="--vMax" type="float" optional="true" label="vMax"/> 110 <param argument="--vMax" type="float" optional="true" label="vMax"/>
110 111 <param name="image_file_format" type="select" label="Image output format">
112 <option value="png" selected="True">png</option>
113 <option value="svg">svg</option>
114 </param>
111 </inputs> 115 </inputs>
112 <outputs> 116 <outputs>
113 <data name="outFileName" from_work_dir="plot.svg" format="svg" label="${tool.name} on ${on_string}"/> 117 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}">
118 <change_format>
119 <when input="image_file_format" value="svg" format="svg" />
120 </change_format>
121 </data>
114 </outputs> 122 </outputs>
115 <tests> 123 <tests>
116 <test> 124 <test>
117 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/> 125 <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/>
118 <param name="region" value="chrX:3000000-3500000"/> 126 <param name="region" value="chrX:3000000-3500000"/>
119 <param name="region2" value="chrX:3100000-3600000"/> 127 <param name="region2" value="chrX:3100000-3600000"/>
120 <param name="log1p" value="True"/> 128 <param name="log1p" value="True"/>
121 <param name="clearMaskedBins" value="True"/> 129 <param name="clearMaskedBins" value="True"/>
122 <param name="whatToShow_select" value="heatmap"/> 130 <param name="whatToShow_select" value="heatmap"/>
123 <output name="outFileName" file="hicPlotMatrix_result1.svg" ftype="svg" compare="sim_size"/> 131 <param name="image_file_format" value="png" />
132 <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
124 </test> 133 </test>
125 </tests> 134 </tests>
126 <help><![CDATA[ 135 <help><![CDATA[
127 136
128 **What it does** 137 **What it does**
129 138
130 Plots a HiC matrix heatmap. 139 Plots a Hi-C matrix heatmap.
131 140
132 ]]></help> 141 ]]></help>
133 <expand macro="citations" /> 142 <expand macro="citations" />
134 </tool> 143 </tool>
135 144