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Hi,

I searched for the options --sortUsingSamples and --clusterUsingSamples in the Galaxy wrapper (plotHeatmap.xml), which are available on the plotHeatmap command-line.

Please note, --clusterUsingSamples I only found in deeptools version 3.4.1 or later.

plotHeatmap --help
[...]
--sortUsingSamples SORTUSINGSAMPLES [SORTUSINGSAMPLES ...]
                        List of sample numbers (order as in matrix), that are
                        used for sorting by --sortUsing, no value uses all
                        samples, example: --sortUsingSamples 1 3 (default:
                        None)

[...]

  --clusterUsingSamples CLUSTERUSINGSAMPLES [CLUSTERUSINGSAMPLES ...]
                        List of sample numbers (order as in matrix), that are
                        used for clustering by --kmeans or --hclust if not
                        given, all samples are taken into account for
                        clustering. Example: --ClusterUsingSamples 1 3
                        (default: None)
[...]

Would it be possible to have those two options to the galaxy wrapper?

Cheers,
-Michael