Mercurial > repos > bgruening > deeptools_plot_heatmap
diff plotHeatmap.xml @ 28:42cb23d80271 draft
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
| author | bgruening |
|---|---|
| date | Fri, 11 Feb 2022 16:10:54 +0000 |
| parents | 751adcc1ce82 |
| children | 25d830337d31 |
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--- a/plotHeatmap.xml Sat Jan 25 05:15:40 2020 -0500 +++ b/plotHeatmap.xml Fri Feb 11 16:10:54 2022 +0000 @@ -34,6 +34,10 @@ --sortRegions '$advancedOpt.sortRegions' #end if + #if $advancedOpt.linesAtTickMarks: + --linesAtTickMarks + #end if + #if $advancedOpt.sortUsing: --sortUsing '$advancedOpt.sortUsing' #end if @@ -71,9 +75,15 @@ #if str($advancedOpt.yMin).strip() != "": --yMin $advancedOpt.yMin #end if - #if $advancedOpt.yMax: + #if str($advancedOpt.yMax).strip() != "": --yMax $advancedOpt.yMax #end if + #if str($advancedOpt.sortUsingSamples).strip() != "": + --sortUsingSamples $advancedOpt.sortUsingSamples + #end if + #if str($advancedOpt.clusterUsingSamples).strip() != "": + --clusterUsingSamples $advancedOpt.clusterUsingSamples + #end if --xAxisLabel '$advancedOpt.xAxisLabel' --yAxisLabel '$advancedOpt.yAxisLabel' @@ -130,6 +140,17 @@ <when value="yes"> <expand macro="sortRegions" /> <expand macro="sortUsing" /> + <param argument="--sortUsingSamples" type="text" + label="List of samples to be used for sorting" + help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting. + If no value is set, it uses all samples. Example: 1 3 (space separated!)" /> + <sanitizer> + <valid initial="string.printable"> + <add value=" "/> + </valid> + </sanitizer> + <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue="" + label="Draw dashed lines in heatmap above all tick marks?" /> <param argument="--averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap" help=""> @@ -162,19 +183,19 @@ help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must be between 0 and 1. A value of 0.0 would be fully transparent." /> - <param argument="--colorList" type="text" value="" size="50" optional="True" + <param argument="--colorList" type="text" value="" optional="True" label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas" help="The color of the heatmaps can be specified as a list of colors separated by comas with not space in between. For example: white,blue white,green will set a color map from white to blue for the first heatmap and for white to green for the next heatmap."/> <expand macro="zMin_zMax" /> - <param argument="--yMin" type="float" value="" size="3" optional="True" + <param argument="--yMin" type="float" value="" optional="True" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/> - <param argument="--yMax" type="float" value="" size="3" optional="True" + <param argument="--yMax" type="float" value="" optional="True" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/> - <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200" + <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" label="The x-axis label" help="" /> - <param argument="--yAxisLabel" type="text" value="genes" size="30" + <param argument="--yAxisLabel" type="text" value="genes" label="The y-axis label for the top panel" help="" /> <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100" @@ -189,17 +210,17 @@ <option value="heatmap and colorbar">heatmap and colorbar</option> </param> - <param argument="--startLabel" type="text" value="TSS" size="10" + <param argument="--startLabel" type="text" value="TSS" 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"." /> - <param argument="--endLabel" type="text" value="TES" size="10" + <param argument="--endLabel" type="text" value="TES" 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)."/> - <param argument="--referencePointLabel" type="text" value="TSS" size="10" + <param argument="--referencePointLabel" type="text" value="TSS" label="Reference point label" 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." /> - <param argument="--samplesLabel" type="text" size="30" + <param argument="--samplesLabel" type="text" label="Labels for the samples (each bigwig) plotted" help="The default is to use the file name of the sample. The sample labels should be separated by spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> @@ -208,7 +229,7 @@ </valid> </sanitizer> </param> - <param argument="--regionsLabel" type="text" size="30" + <param argument="--regionsLabel" type="text" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by space is required. If a label itself contains a space, then quotes are needed. @@ -222,6 +243,15 @@ 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."/> <expand macro="kmeans_clustering" /> + <param argument="--clusterUsingSamples" type="text" + label="List of samples to be used for clustering" + help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering. + If no value is set, it uses all samples. Example: 1 3 (space separated!)"/> + <sanitizer> + <valid initial="string.printable"> + <add value=" "/> + </valid> + </sanitizer> </when> </conditional> </inputs>