Mercurial > repos > bgruening > deeptools
diff plotCorrelation.xml @ 65:9bee2c86eeb1 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
| author | iuc |
|---|---|
| date | Mon, 25 May 2015 05:16:10 -0400 |
| parents | 1d932daaa198 |
| children |
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--- a/plotCorrelation.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/plotCorrelation.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0"> <description>creates a heatmap for a score associated to genomic regions</description> - <expand macro="requirements"/> - <expand macro="stdio" /> <macros> <token name="@BINARY@">heatmapper</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements"/> <command> <![CDATA[ heatmapper @@ -76,7 +75,7 @@ --refPointLabel '$advancedOpt.referencePointLabel' --regionsLabel '$advancedOpt.regionsLabel' - #if str($advancedOpt.plotTitle.value) != "None": + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #end if @@ -110,13 +109,6 @@ <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> - <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" - label="Plot the correlation value" - help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/> - - - - <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> <param name="yMax" type="float" value="" size="3" @@ -142,27 +134,33 @@ <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" - 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"." /> + 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)" /> <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" - help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/> + help="[only for scale-regions mode] Label shown in the plot for the region end. (--endLabel)"/> <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" - help ="[only for scale-regions mode] 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." /> + help ="[only for scale-regions mode] 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)" /> <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" - 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."> + 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)"> <sanitizer> <valid initial="string.printable"> </valid> </sanitizer> </param> - <param name="plotTitle" type="text" value="" size="30" - label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" /> - <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" - label="Do one plot per group" - 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. If this option is set, each group will get its own plot, stacked on top of each other."/> + + <expand macro="plotTitle" /> + <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" + label="Do one plot per group" + 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. + If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/> <expand macro="kmeans_clustering" /> </when>