Mercurial > repos > bgruening > deeptools_plot_heatmap

comparison plotHeatmap.xml @ 17:0d6dfbd66443 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author bgruening
date Thu, 15 Feb 2018 08:29:45 -0500
parents c1ff5c446073
children 010e58e9d822
comparison
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16:4a42f2445e42 17:0d6dfbd66443
44 44
45 #if str($advancedOpt.missingDataColor.value) != "None": 45 #if str($advancedOpt.missingDataColor.value) != "None":
46 --missingDataColor '$advancedOpt.missingDataColor' 46 --missingDataColor '$advancedOpt.missingDataColor'
47 #end if 47 #end if
48 48
49 #if str($advancedOpt.colorMap).strip() != "": 49 #set colorMap = []
50 --colorMap #echo " ".join(str($advancedOpt.colorMap).strip().split(","))# 50 #for $cmap in $advancedOpt.colorMapRepeat:
51 #end if 51 #silent $colorMap.append(str($cmap.colorMap))
52 #end for
53 #if len($colorMap) > 0:
54 --colorMap #echo " ".join($colorMap)#
55 #end if
56
52 --alpha '$advancedOpt.alpha' 57 --alpha '$advancedOpt.alpha'
53 #if str($advancedOpt.colorList).strip() != "": 58 #if str($advancedOpt.colorList).strip() != "":
54 --colorList $advancedOpt.colorList 59 --colorList $advancedOpt.colorList
55 #end if 60 #end if
56 61
90 #end if 95 #end if
91 96
92 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": 97 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
93 --plotTitle '$advancedOpt.plotTitle' 98 --plotTitle '$advancedOpt.plotTitle'
94 #end if 99 #end if
100
101 --labelRotation '$advancedOpt.labelRotation'
95 102
96 $advancedOpt.perGroup 103 $advancedOpt.perGroup
97 104
98 @KMEANS_CLUSTERING@ 105 @KMEANS_CLUSTERING@
99 106
134 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. 141 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
135 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). 142 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
136 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. 143 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
137 Alternatively colors can be specified using the #rrggbb notation." /> 144 Alternatively colors can be specified using the #rrggbb notation." />
138 145
139 <expand macro="colorMap" /> 146 <repeat name="colorMapRepeat" title="Colormap to use for each sample"
147 help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples).">
148 <expand macro="colorMap" />
149 </repeat>
140 <param argument="--alpha" type="float" value="1.0" min="0.0" 150 <param argument="--alpha" type="float" value="1.0" min="0.0"
141 max="1.0" optional="True" 151 max="1.0" optional="True"
142 label="Alpha channel (transparency)" 152 label="Alpha channel (transparency)"
143 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must 153 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
144 be between 0 and 1. A value of 0.0 would be fully transparent." /> 154 be between 0 and 1. A value of 0.0 would be fully transparent." />
194 help="If more than one region is being plotted a list of labels separated by space is required. 204 help="If more than one region is being plotted a list of labels separated by space is required.
195 If a label itself contains a space, then quotes are needed. 205 If a label itself contains a space, then quotes are needed.
196 For example, label_1 &quot;label 2&quot;" /> 206 For example, label_1 &quot;label 2&quot;" />
197 207
198 <expand macro="plotTitle" /> 208 <expand macro="plotTitle" />
209 <expand macro="labelRotation" />
199 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue="" 210 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
200 label="Make one plot per group of regions" 211 label="Make one plot per group of regions"
201 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/> 212 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>
202 213
203 <expand macro="kmeans_clustering" /> 214 <expand macro="kmeans_clustering" />