deeptools: heatmapper.xml annotate

annotate heatmapper.xml @ 31:7889d260cc37 draft default tip

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty

author	bgruening
date	Wed, 21 Oct 2015 02:50:24 -0400
parents	5231f398d784
children

rev	line source
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	1 <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0">
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	2 <description>creates a heatmap for a score associated to genomic regions</description>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	3 <macros>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	4 <token name="@BINARY@">heatmapper</token>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	5 <import>deepTools_macros.xml</import>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	6 </macros>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	7 <expand macro="requirements"/>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	8 <command>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	9 <![CDATA[
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	10 heatmapper
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	11
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	12 --matrixFile $matrixFile
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	13 --outFileName $outFileName
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	14
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	15 #if $output.showOutputSettings == "yes"
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	16 --plotFileFormat $output.outFileFormat
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	17 #if $outFileNameData:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	18 --outFileNameData '$outFileNameData'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	19 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	20
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	21 #if $outFileNameMatrix:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	22 --outFileNameMatrix '$outFileNameMatrix'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	23 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	24
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	25 #if $outFileSortedRegions:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	26 --outFileSortedRegions '$outFileSortedRegions'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	27 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	28 #else
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	29 --plotFileFormat 'png'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	30 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	31
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	32 #if $advancedOpt.showAdvancedOpt == "yes"
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	33 #if $advancedOpt.sortRegions:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	34 --sortRegions '$advancedOpt.sortRegions'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	35 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	36
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	37 #if $advancedOpt.sortUsing:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	38 --sortUsing '$advancedOpt.sortUsing'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	39 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	40
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	41 #if $advancedOpt.averageTypeSummaryPlot:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	43 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	44
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	45 #if str($advancedOpt.missingDataColor.value) != "None":
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	46 --missingDataColor '$advancedOpt.missingDataColor'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	47 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	48
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	49 --colorMap '$advancedOpt.colorMap'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	50
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	51 #if str($advancedOpt.zMin).strip() != "":
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	52 --zMin $advancedOpt.zMin
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	53 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	54 #if $advancedOpt.zMax:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	55 --zMax $advancedOpt.zMax
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	56 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	57
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	58 #if str($advancedOpt.yMin).strip() != "":
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	59 --yMin $advancedOpt.yMin
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	60 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	61 #if $advancedOpt.yMax:
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	62 --yMax $advancedOpt.yMax
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	63 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	64
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	65 --xAxisLabel '$advancedOpt.xAxisLabel'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	66 --yAxisLabel '$advancedOpt.yAxisLabel'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	67
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	68 --heatmapWidth $advancedOpt.heatmapWidth
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	69 --heatmapHeight $advancedOpt.heatmapHeight
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	70
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	71 --whatToShow '$advancedOpt.whatToShow'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	72
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	73 --startLabel '$advancedOpt.startLabel'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	74 --endLabel '$advancedOpt.endLabel'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	75 --refPointLabel '$advancedOpt.referencePointLabel'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	76 --regionsLabel '$advancedOpt.regionsLabel'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	77
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	78 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	79 --plotTitle '$advancedOpt.plotTitle'
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	80 #end if
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	81
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	82 $advancedOpt.onePlotPerGroup
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	83
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	84 @KMEANS_CLUSTERING@
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	85
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	86 #end if
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	87 ]]>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	88 </command>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	89 <inputs>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	90 <param name="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	91
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	92 <expand macro="input_graphic_output_settings">
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	93 <expand macro="input_image_file_format" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	94 <expand macro="input_save_matrix_values" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	95 </expand>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	96
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	97 <conditional name="advancedOpt" >
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	98 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	99 <option value="no" selected="true">no</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	100 <option value="yes">yes</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	101 </param>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	102 <when value="no" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	103 <when value="yes">
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	104 <param name="sortRegions" type="select" label="Sort regions"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	105 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region. (--sortRegions)">
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	106 <option value="no">no ordering</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	107 <option value="descend" selected="true">descending order</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	108 <option value="ascend">ascending order</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	109 </param>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	110
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	111 <param name="sortUsing" type="select" label="Method used for sorting"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	112 help="For each row the method is computed. (--sortUsing)">
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	113 <option value="mean" selected="true">mean</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	114 <option value="median">median</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	115 <option value="min">min</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	116 <option value="max">max</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	117 <option value="sum">sum</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	118 <option value="region_length">region length</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	119 </param>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	120
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	121 <param name="averageTypeSummaryPlot" type="select"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	122 label="Type of statistic that should be plotted in the summary image above the heatmap"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	123 help="(--averageTypeSummaryPlot)">
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	124 <option value="mean" selected="true">mean</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	125 <option value="median">median</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	126 <option value="min">min</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	127 <option value="max">max</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	128 <option value="sum">sum</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	129 <option value="std">std</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	130 </param>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	131
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	132 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	133 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	134 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).
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	135 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	136 Alternatively colors can be specified using the #rrggbb notation. (--missingDataColor)" />
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	137
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	138 <expand macro="colormap" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	139
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	140 <param name="zMin" type="float" value="" size="3"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	141 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help="(--zMin)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	142 <param name="zMax" type="float" value="" size="3"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	143 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help="(--zMax)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	144 <param name="yMin" type="float" value="" size="3"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	145 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help="(--yMin)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	146 <param name="yMax" type="float" value="" size="3"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	147 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help="(--yMax)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	148 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	149 label="Description for the x-axis label" help="(--xAxisLabel)"/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	150 <param name="yAxisLabel" type="text" value="genes" size="30"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	151 label="Description for the y-axis label for the top panel" help="(--yAxisLabel)"/>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	152
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	153 <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	154 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	155 <param name="heatmapHeight" type="float" value="25" min="3" max="100"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	156 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	157
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	158 <param name="whatToShow" type="select" label="What to show"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	159 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar. (--whatToShow)">
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	160 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	161 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	162 <option value="heatmap only">heatmap only</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	163 <option value="heatmap and colorbar">heatmap and colorbar</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	164 <option value="colorbar only">colorbar only</option>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	165 </param>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	166
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	167 <param name="startLabel" type="text" value="TSS" size="10"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	168 label="Label for the region start"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	169 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start". (--startLabel)" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	170 <param name="endLabel" type="text" value="TES" size="10"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	171 label="Label for the region end"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	172 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	173
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	174 <param name="referencePointLabel" type="text" value="TSS" size="10"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	175 label="Reference point label"
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	176 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. "peak start" etc. (--referencePointLabel)" />
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	177 <param name="regionsLabel" type="text" value="genes" size="30"
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	178 label="Labels for the regions plotted in the heatmap"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	179 help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)">
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	180 <sanitizer>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	181 <valid initial="string.printable">
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	182 </valid>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	183 </sanitizer>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	184 </param>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	185 <expand macro="plotTitle" />
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	186 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	187 label="Do one plot per group"
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	188 help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default.
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	189 If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	190
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	191 <expand macro="kmeans_clustering" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	192 </when>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	193 </conditional>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	194 </inputs>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	195 <outputs>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	196 <expand macro="output_image_file_format" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	197 <expand macro="output_graphic_outputs" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	198 <expand macro="output_save_matrix_values" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	199 </outputs>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	200 <tests>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	201 <test>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	202 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	203 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	204 </test>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	205 </tests>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	206 <help>
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	207 <![CDATA[
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	208 What it does
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	209
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	210 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	211 Like profiler, it requires that computeMatrix was run first to calculate the values.
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	212
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	213 We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	214 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	215 groups with similar read distributions that you expect and the algorithm will do the sorting for you.
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	216
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	217 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	218
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	219
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	220 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	221 :alt: Heatmap of RNA Polymerase II ChIP-seq
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	222
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	223
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	224 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	225
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	226
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	227 -----
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	228
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	229 @REFERENCES@
30 5231f398d784 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty bgruening parents: 29 diff changeset	230 ]]>
29 3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	231 </help>
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	232 <expand macro="citations" />
3a2aab18a217 Uploaded bgruening parents: 28 diff changeset	233 </tool>

Mercurial > repos > bgruening > deeptools

annotate heatmapper.xml @ 31:7889d260cc37 draft default tip