Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

comparison hicPlotMatrix.xml @ 15:b553d14a7845 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 06:46:07 -0400
parents fe13295d0329
children 7babd8a46fe0
comparison
equal deleted inserted replaced
14:fe13295d0329 15:b553d14a7845
14 #set $pca = '' 14 #set $pca = ''
15 #end if 15 #end if
16 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext && 16 ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
17 @BINARY@ 17 @BINARY@
18 18
19 19
20 --matrix 'matrix.$matrix_h5_cooler.ext' 20 --matrix 'matrix.$matrix_h5_cooler.ext'
21 21
22 #if $title and $title is not None: 22 #if $title and $title is not None:
23 --title '$title' 23 --title '$title'
24 #end if 24 #end if
57 #end if 57 #end if
58 58
59 #if $vMax: 59 #if $vMax:
60 --vMax $vMax 60 --vMax $vMax
61 #end if 61 #end if
62 62
63 #if str($pca_conditional.pca_type) == 'bigwig': 63 #if str($pca_conditional.pca_type) == 'bigwig':
64 --vMinBigwig $pca_conditional.vMinBigwig 64 #if $pca_conditional.vMinBigwig:
65 --vMaxBigwig $pca_conditional.vMaxBigwig 65 --vMinBigwig $pca_conditional.vMinBigwig
66 #end if
67 #if $pca_conditional.vMaxBigwig:
68 --vMaxBigwig $pca_conditional.vMaxBigwig
69 #end if
66 $pca_conditional.flipBigwigSign 70 $pca_conditional.flipBigwigSign
67 --scaleFactorBigwig $pca_conditional.scaleFactorBigwig 71
72 #if $pca_conditional.scaleFactorBigwig:
73 --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
74 #end if
68 $pca_conditional.bigwigAdditionalVerticalAxis 75 $pca_conditional.bigwigAdditionalVerticalAxis
69 #end if 76 #end if
70 $pca 77 $pca
71 #if $dpi: 78 #if $dpi:
72 --dpi $dpi 79 --dpi $dpi
73 #end if 80 #end if
81
82 #if $fontSize:
83 --fontSize $fontSize
84 #end if
85
86 #if $rotationX:
87 --rotationX $rotationX
88 #end if
89
90 #if $rotationY:
91 --rotationY $rotationY
92 #end if
74 93
75 #if $loops: 94 #if $loops:
76 --loops '$loops' 95 --loops '$loops'
77 #end if 96 #end if
78 && mv plot.$image_file_format plot 97 && mv plot.$image_file_format plot
100 help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/> 119 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" 120 <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"/> 121 help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
103 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/> 122 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
104 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/> 123 <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>
124 <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis."/>
125 <param argument="--rotationX" type="integer" optional="true" label="Rotate x-labels by degree" help="Rotation in degrees for the labels of x-axis."/>
126 <param argument="--rotationY" type="integer" optional="true" label="Rotate y-labels by degree" help="Rotation in degrees for the labels of y-axis."/>
105 127
106 <expand macro="colormap" /> 128 <expand macro="colormap" />
107 129
108 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/> 130 <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score."/>
109 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/> 131 <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score."/>
185 <param name="dpi" value="10" /> 207 <param name="dpi" value="10" />
186 208
187 <param name="image_file_format" value="svg" /> 209 <param name="image_file_format" value="svg" />
188 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/> 210 <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/>
189 </test> 211 </test>
190 212
191 </tests> 213 </tests>
192 <help><![CDATA[ 214 <help><![CDATA[
193 Contact matrix plot 215 Contact matrix plot
194 ======================= 216 =======================
195 217