Mercurial > repos > bgruening > deeptools
annotate profiler.xml @ 80:be73bb8a1303 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 02:51:49 -0400 |
| parents | 5f7c4d7930e2 |
| children |
| rev | line source |
|---|---|
| 61 | 1 <tool id="deeptools_profiler" name="profiler" version="@WRAPPER_VERSION@.0"> |
| 2 <description> | |
| 3 creates a profile plot for a score associated to genomic regions | |
| 4 </description> | |
| 5 <macros> | |
| 6 <token name="@BINARY@">profiler</token> | |
| 7 <import>deepTools_macros.xml</import> | |
| 8 </macros> | |
|
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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9 <expand macro="requirements" /> |
| 61 | 10 <command> |
| 11 <![CDATA[ | |
| 12 profiler | |
| 13 | |
| 14 --matrixFile $matrixFile | |
| 15 --outFileName $outFileName | |
| 16 | |
| 17 #if $output.showOutputSettings == "yes" | |
| 18 --plotFileFormat $output.outFileFormat | |
| 19 | |
| 20 #if $output.saveData: | |
| 21 --outFileNameData '$outFileNameData' | |
| 22 #end if | |
| 23 | |
| 24 #if $output.saveSortedRegions: | |
| 25 --outFileSortedRegions '$outFileSortedRegions' | |
| 26 #end if | |
| 27 #else | |
| 28 --plotFileFormat 'png' | |
| 29 #end if | |
| 30 | |
| 31 #if $scaleRegions.showScaleRegionsOpt == "yes": | |
| 32 --startLabel '$scaleRegions.startLabel' | |
| 33 --endLabel '$scaleRegions.endLabel' | |
| 34 #end if | |
| 35 | |
| 36 #if $advancedOpt.showAdvancedOpt == "yes": | |
| 37 #if $advancedOpt.averageType: | |
| 38 --averageType '$advancedOpt.averageType' | |
| 39 #end if | |
| 40 --plotHeight $advancedOpt.plotHeight | |
| 41 --plotWidth $advancedOpt.plotWidth | |
| 42 --plotType $advancedOpt.plotType | |
| 43 | |
| 44 --regionsLabel '$advancedOpt.regionsLabel' | |
| 45 | |
|
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "": |
| 61 | 47 --plotTitle '$advancedOpt.plotTitle' |
| 48 #end if | |
| 49 | |
| 50 #if str($advancedOpt.colors).strip() != "": | |
| 51 --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# | |
| 52 #end if | |
| 53 | |
| 54 $advancedOpt.onePlotPerGroup | |
| 55 | |
| 56 #if $advancedOpt.yMin: | |
| 57 --yMin $advancedOpt.yMin | |
| 58 #end if | |
| 59 #if $advancedOpt.yMax: | |
| 60 --yMax $advancedOpt.yMax | |
| 61 #end if | |
| 62 | |
| 63 --xAxisLabel '$advancedOpt.xAxisLabel' | |
| 64 #if str($advancedOpt.yAxisLabel.value) != "None": | |
| 65 --yAxisLabel '$advancedOpt.yAxisLabel' | |
| 66 #end if | |
| 67 | |
| 68 @KMEANS_CLUSTERING@ | |
| 69 | |
| 70 #end if | |
| 71 ]]> | |
| 72 </command> | |
| 73 <inputs> | |
|
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5f7c4d7930e2
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
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74 <param name="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool"/> |
| 61 | 75 <conditional name="scaleRegions"> |
| 76 <param name="showScaleRegionsOpt" type="select" label="The input matrix was computed in scale-regions mode"> | |
| 77 <option value="no" selected="true">no</option> | |
| 78 <option value="yes">yes</option> | |
| 79 </param> | |
| 80 <when value="no" /> | |
| 81 <when value="yes"> | |
| 82 <param name="startLabel" type="text" value="TSS" size="10" | |
| 83 label="Label for the region start" | |
|
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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84 help ="[only for scale-regions mode] Label shown in the plot |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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changeset
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85 for the start of the region. Default is TSS (transcription start site), |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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86 but could be changed to anything, e.g. "peak start"." /> |
| 61 | 87 <param name="endLabel" type="text" value="TES" size="10" |
| 88 label="Label for the region end" | |
| 89 help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/> | |
| 90 </when> | |
| 91 </conditional> | |
| 92 | |
| 93 <expand macro="input_graphic_output_settings"> | |
| 94 <expand macro="input_image_file_format" /> | |
| 95 </expand> | |
| 96 | |
| 97 <conditional name="advancedOpt"> | |
| 98 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
| 99 <option value="no" selected="true">no</option> | |
| 100 <option value="yes">yes</option> | |
| 101 </param> | |
| 102 <when value="no" /> | |
| 103 <when value="yes"> | |
| 104 <param name="averageType" type="select" label="Define the type of statistic that should be used for the profile."> | |
| 105 <option value="mean" selected="true">mean</option> | |
| 106 <option value="median">median</option> | |
| 107 <option value="min">min</option> | |
| 108 <option value="max">max</option> | |
| 109 <option value="sum">sum</option> | |
| 110 <option value="std">std</option> | |
| 111 </param> | |
| 112 <param name="plotHeight" type="integer" value="5" min="3" | |
| 113 label="Plot height" | |
| 114 help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." /> | |
| 115 <param name="plotWidth" type="integer" value="8" min="1" | |
| 116 label="Plot width" | |
| 117 help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." /> | |
| 118 <param name="plotType" type="select" label="Plot type" | |
|
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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119 help="For the summary plot (profile) only. The "lines" option will |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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120 plot the profile line based on the average type selected. The "fill" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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121 option fills the region between zero and the profile curve. The fill in color is |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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changeset
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122 semi transparent to distinguish different profiles. The "add standard error" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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123 option colors the region between the profile and the standard error of the data. |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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124 As in the case of fill, a semi-transparent color is used. |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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125 The option "overlapped_lines" plots each region values, one on top of |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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126 the other; this option only works if "one plot per proup" is set."> |
| 61 | 127 <option value="lines" selected="true">lines</option> |
| 128 <option value="fill">fill</option> | |
| 129 <option value="se">add standard error</option> | |
| 130 <option value="overlapped_lines">overlapped lines</option> | |
| 131 </param> | |
| 132 <param name="regionsLabel" type="text" value="genes" size="30" | |
| 133 label="Labels for the regions plotted in the heatmap" | |
|
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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134 help="If more than one region is being plotted a list of labels separated |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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135 by comma and limited by quotes, is required. For example, "label1, label2"."/> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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136 |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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137 <expand macro="plotTitle" /> |
| 61 | 138 <param name="colors" type="text" value="" size="40" |
| 139 label="List of colors to use for the plotted lines" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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140 help="Color names and html hex strings (e.g. #eeff22) are accepted. |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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141 The color names should be given separated by spaces. (--colors red blue green)"> |
| 61 | 142 <validator type="expression" |
| 143 message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> | |
| 144 </param> | |
| 145 | |
| 146 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" | |
| 147 label="Do one plot per group" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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148 help="When the region file contains groups separated by "#", the default is |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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149 to plot the averages for the distinct plots in one plot. If this option is set, each group |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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150 will get its own plot, stacked on top of each other."/> |
| 61 | 151 <param name="yMin" type="float" value="" size="3" optional="true" |
| 152 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> | |
| 153 <param name="yMax" type="float" value="" size="3" optional="true" | |
| 154 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" /> | |
| 155 <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" | |
| 156 label="Description for the x-axis label" /> | |
| 157 <param name="yAxisLabel" type="text" value="" size="50" | |
| 158 label="Description for the y-axis label for the top panel" /> | |
| 159 | |
| 160 <expand macro="kmeans_clustering" /> | |
| 161 | |
| 162 </when> | |
| 163 </conditional> | |
| 164 </inputs> | |
| 165 <outputs> | |
| 166 <expand macro="output_image_file_format" /> | |
| 167 <expand macro="output_graphic_outputs" /> | |
| 168 </outputs> | |
|
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169 <tests> |
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170 <test> |
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171 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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172 <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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173 </test> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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174 </tests> |
| 61 | 175 <help> |
| 176 <![CDATA[ | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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177 |
| 61 | 178 **What it does** |
| 179 | |
| 180 This tool plots the average enrichments over all genomic | |
| 181 regions supplied to computeMarix. It requires that computeMatrix was successfully run. | |
| 182 It is a very useful complement to the heatmapper, especially in cases when you want to | |
| 183 compare the scores for many different groups. Like heatmapper, profiler does not change the | |
| 184 values that were compute by computeMatrix, but you can choose between | |
| 185 many different ways to color and display the plots. | |
| 186 | |
| 187 | |
| 188 .. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png | |
| 189 :alt: Meta-gene profile of Rna Polymerase II | |
| 190 | |
| 191 | |
| 192 You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler | |
| 193 | |
| 194 | |
| 195 ----- | |
| 196 | |
| 197 @REFERENCES@ | |
| 198 ]]> | |
| 199 </help> | |
| 200 <expand macro="citations" /> | |
| 201 </tool> |