Mercurial > repos > bgruening > deeptools_plot_heatmap

comparison plotHeatmap.xml @ 8:ca218dae7902 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Mon, 19 Sep 2016 17:49:56 -0400
parents 6a247ae015cc
children c1ff5c446073
comparison
equal deleted inserted replaced
7:e57bfadcab30 8:ca218dae7902
19 #end if 19 #end if
20 20
21 #if $outFileSortedRegions: 21 #if $outFileSortedRegions:
22 --outFileSortedRegions "$outFileSortedRegions" 22 --outFileSortedRegions "$outFileSortedRegions"
23 #end if 23 #end if
24
25 #if $output.dpi:
26 --dpi "$output.dpi"
27 #end if
24 #else 28 #else
25 --plotFileFormat 'png' 29 --plotFileFormat 'png'
26 #end if 30 #end if
27 31
28 #if $advancedOpt.showAdvancedOpt == "yes" 32 #if $advancedOpt.showAdvancedOpt == "yes"
40 44
41 #if str($advancedOpt.missingDataColor.value) != "None": 45 #if str($advancedOpt.missingDataColor.value) != "None":
42 --missingDataColor '$advancedOpt.missingDataColor' 46 --missingDataColor '$advancedOpt.missingDataColor'
43 #end if 47 #end if
44 48
45 --colorMap '$advancedOpt.colorMap' 49 #if str($advancedOpt.colorMap).strip() != "":
50 --colorMap #echo " ".join(str($advancedOpt.colorMap).strip().split(","))#
51 #end if
52 --alpha '$advancedOpt.alpha'
53 #if str($advancedOpt.colorList).strip() != "":
54 --colorList $advancedOpt.colorList
55 #end if
46 56
47 #if str($advancedOpt.zMin).strip() != "": 57 #if str($advancedOpt.zMin).strip() != "":
48 --zMin $advancedOpt.zMin 58 --zMin $advancedOpt.zMin
49 #end if 59 #end if
50 #if $advancedOpt.zMax: 60 #if str($advancedOpt.zMax).strip() != "":
51 --zMax $advancedOpt.zMax 61 --zMax $advancedOpt.zMax
52 #end if 62 #end if
53 63
54 #if str($advancedOpt.yMin).strip() != "": 64 #if str($advancedOpt.yMin).strip() != "":
55 --yMin $advancedOpt.yMin 65 --yMin $advancedOpt.yMin
89 99
90 #end if 100 #end if
91 ]]> 101 ]]>
92 </command> 102 </command>
93 <inputs> 103 <inputs>
94 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/> 104 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
105 label="Matrix file from the computeMatrix tool" help=""/>
95 106
96 <expand macro="input_graphic_output_settings"> 107 <expand macro="input_graphic_output_settings">
97 <expand macro="input_image_file_format" /> 108 <expand macro="input_image_file_format" />
109 <expand macro="output_dpi" />
98 <expand macro="input_save_matrix_values" /> 110 <expand macro="input_save_matrix_values" />
99 </expand> 111 </expand>
100 112
101 <conditional name="advancedOpt" > 113 <conditional name="advancedOpt" >
102 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 114 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
123 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). 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).
124 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. 136 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
125 Alternatively colors can be specified using the #rrggbb notation." /> 137 Alternatively colors can be specified using the #rrggbb notation." />
126 138
127 <expand macro="colorMap" /> 139 <expand macro="colorMap" />
128 140 <param argument="--alpha" type="float" value="1.0" min="0.0"
129 <param argument="--zMin" type="float" value="" size="3" optional="True" 141 max="1.0" optional="True"
130 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/> 142 label="Alpha channel (transparency)"
131 <param argument="--zMax" type="float" value="" size="3" optional="True" 143 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
132 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/> 144 be between 0 and 1. A value of 0.0 would be fully transparent." />
145
146 <param argument="--colorList" type="text" value="" size="50" optional="True"
147 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
148 help="The color of the heatmaps can be specified as a list of colors separated by comas with
149 not space in between. For example: white,blue white,green will set a color map from white
150 to blue for the first heatmap and for white to green for the next heatmap."/>
151 <expand macro="zMin_zMax" />
133 <param argument="--yMin" type="float" value="" size="3" optional="True" 152 <param argument="--yMin" type="float" value="" size="3" optional="True"
134 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/> 153 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
135 <param argument="--yMax" type="float" value="" size="3" optional="True" 154 <param argument="--yMax" type="float" value="" size="3" optional="True"
136 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/> 155 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
137 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200" 156 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"