Mercurial > repos > bgruening > deeptools_plot_correlation

comparison plotCorrelation.xml @ 40:7f7a2ae8a310 draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
author bgruening
date Fri, 24 Jan 2020 07:32:34 +0000
parents 659b08d0c4b1
children a68c2640aee5
comparison
equal deleted inserted replaced
39:7f265e1ced94 40:7f7a2ae8a310
16 @HEATMAP_OPTIONS@ 16 @HEATMAP_OPTIONS@
17 --plotWidth $plotting_type.plotWidth 17 --plotWidth $plotting_type.plotWidth
18 --plotHeight $plotting_type.plotHeight 18 --plotHeight $plotting_type.plotHeight
19 #else: 19 #else:
20 --plotTitle '$plotting_type.plotTitle' 20 --plotTitle '$plotting_type.plotTitle'
21 #if str($plotting_type.xRange) != '': 21 #if str($plotting_type.xrange_conditional.xrange_select) == 'yes':
22 --xRange '$plotting_type.xRange' 22 --xRange $plotting_type.xrange_conditional.xRange_min $plotting_type.xrange_conditional.xRange_max
23 #end if 23 #end if
24 #if str($plotting_type.yRange) != '': 24 #if str($plotting_type.yrange_conditional.yrange_select) == 'yes':
25 --yRange '$plotting_type.yRange' 25 --yRange $plotting_type.yrange_conditional.yRange_min $plotting_type.yrange_conditional.yRange_max
26 #end if 26 #end if
27 $plotting_type.log1p 27 $plotting_type.log1p
28 #end if 28 #end if
29 $skipZeros 29 $skipZeros
30 --plotFileFormat '$outFileFormat' 30 --plotFileFormat '$outFileFormat'
48 <expand macro="heatmap_options" /> 48 <expand macro="heatmap_options" />
49 <expand macro="plotWidthHeight" PLOTWIDTH="11.0" PLOTHEIGHT="9.5" /> 49 <expand macro="plotWidthHeight" PLOTWIDTH="11.0" PLOTHEIGHT="9.5" />
50 </when> 50 </when>
51 <when value="scatterplot"> 51 <when value="scatterplot">
52 <expand macro="plotTitle" /> 52 <expand macro="plotTitle" />
53 <param argument="--xRange" type="text" value="" optional="true" 53 <conditional name="xrange_conditional">
54 label="X axis range" 54 <param type="select" name="xrange_select" label="Manually set X axis range?">
55 help="X axis range, the default scales these such that the full range of dots is displayed. The input should be two integers separated by a space." /> 55 <option value="no" selected="True">No</option>
56 <param argument="--yRange" type="text" value="" optional="true" 56 <option value="yes">Yes</option>
57 label="Y axis range" 57 </param>
58 help="Y axis range, the default scales these such that the full range of dots is displayed. The input should be two integers separated by a space." /> 58 <when value="yes">
59 <param name="xRange_min" type="integer" value="0" label="X axis minimum value"
60 help="X axis minimum value. Not specifying this scales these such that the full range of dots is displayed." />
61 <param name="xRange_max" type="integer" value="1000" label="X axis maximum value"
62 help="X axis maximum value. Not specifying this scales these such that the full range of dots is displayed." />
63 </when>
64 <when value="no" />
65 </conditional>
66 <conditional name="yrange_conditional">
67 <param type="select" name="yrange_select" label="Manually set Y axis range?">
68 <option value="no" selected="True">No</option>
69 <option value="yes">Yes</option>
70 </param>
71 <when value="yes">
72 <param name="yRange_min" type="integer" value="0" label="Y axis minimum value"
73 help="Y axis minimum value. Not specifying this scales these such that the full range of dots is displayed." />
74 <param name="yRange_max" type="integer" value="1000" label="Y axis maximum value"
75 help="Y axis maximum value. Not specifying this scales these such that the full range of dots is displayed." />
76 </when>
77 <when value="no" />
78 </conditional>
59 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" 79 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue=""
60 label="Log transform" 80 label="Log transform"
61 help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." /> 81 help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." />
62 </when> 82 </when>
63 </conditional> 83 </conditional>