# HG changeset patch # User bgruening # Date 1450809704 18000 # Node ID 59f925c67e2fc578a6645071c8ef052b8798ab2f # Parent 2550686f928b5015162f0c1fc8c12171e30464d8 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty diff -r 2550686f928b -r 59f925c67e2f deepTools_macros.xml --- a/deepTools_macros.xml Mon Dec 21 19:04:02 2015 -0500 +++ b/deepTools_macros.xml Tue Dec 22 13:41:44 2015 -0500 @@ -40,10 +40,10 @@ - #if $plotting_type.zMin: + #if str($plotting_type.zMin) != "": --zMin $plotting_type.zMin #end if - #if $plotting_type.zMax: + #if str($plotting_type.zMax) != "": --zMax $plotting_type.zMax #end if --colorMap '$plotting_type.colorMap' @@ -107,7 +107,11 @@ + help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. + Only works for data that is not grouped, otherwise only the first group will be clustered. + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) + if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/> @@ -408,7 +412,6 @@ - @@ -456,14 +459,6 @@ - - - (( - output['showOutputSettings'] == 'yes' and - output['saveData'] is True - )) - - (( diff -r 2550686f928b -r 59f925c67e2f plotHeatmap.xml --- a/plotHeatmap.xml Mon Dec 21 19:04:02 2015 -0500 +++ b/plotHeatmap.xml Tue Dec 22 13:41:44 2015 -0500 @@ -32,7 +32,7 @@ #if $advancedOpt.sortRegions: --sortRegions '$advancedOpt.sortRegions' #end if - + #if $advancedOpt.sortUsing: --sortUsing '$advancedOpt.sortUsing' #end if @@ -69,7 +69,7 @@ --whatToShow '$advancedOpt.whatToShow' - --startLabel '$advancedOpt.startLabel' + --startLabel '$advancedOpt.startLabel' --endLabel '$advancedOpt.endLabel' --refPointLabel '$advancedOpt.referencePointLabel' --regionsLabel '$advancedOpt.regionsLabel' @@ -78,7 +78,7 @@ --plotTitle '$advancedOpt.plotTitle' #end if - $advancedOpt.onePlotPerGroup + $advancedOpt.perGroup @KMEANS_CLUSTERING@ @@ -113,7 +113,7 @@ - - - - @@ -167,10 +165,12 @@ - + @@ -199,19 +199,17 @@ The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. Like profiler, it requires that computeMatrix was run first to calculate the values. - -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 -with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of -groups with similar read distributions that you expect and the algorithm will do the sorting for you. -Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows +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 with the different coloring options. The most powerful option is the k-means/hirarchichal clustering +where you simply need to indicate the number of groups with similar read distributions that you expect and the algorithm will do the sorting for you. .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png :alt: Heatmap of RNA Polymerase II ChIP-seq -You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper +You can find more details on the tool on the plotHeatmap doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/plotHeatmap.html ----- diff -r 2550686f928b -r 59f925c67e2f static/images/plotCorrelation_galaxy_bw_heatmap_output.png Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed