--- a/filter.xml	Thu Dec 05 12:09:12 2019 +0000
+++ b/filter.xml	Thu Dec 12 14:21:41 2019 +0000
@@ -113,12 +113,12 @@
         <expand macro="inputs_anndata"/>
         <conditional name="method">
             <param argument="method" type="select" label="Method used for filtering">
-                <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`</option>
-                <option value="pp.filter_genes">Filter genes based on number of cells or counts, using `pp.filter_genes`</option>
-                <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using `tl.filter_rank_genes_groups`</option>
-                <option value="pp.highly_variable_genes">, using `tl.highly_variable_genes`</option>
-                <option value="pp.subsample">Subsample to a fraction of the number of observations, using `pp.subsample`</option>
-                <option value="pp.downsample_counts">Downsample counts from count matrix, using `pp.downsample_counts`</option>
+                <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
+                <option value="pp.filter_genes">Filter genes based on number of cells or counts, using 'pp.filter_genes'</option>
+                <option value="tl.filter_rank_genes_groups">Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories, using 'tl.filter_rank_genes_groups'</option>
+                <option value="pp.highly_variable_genes">Annotate (and filter) highly variable genes, using 'pp.highly_variable_genes'</option>
+                <option value="pp.subsample">Subsample to a fraction of the number of observations, using 'pp.subsample'</option>
+                <option value="pp.downsample_counts">Downsample counts from count matrix, using 'pp.downsample_counts'</option>
             </param>
             <when value="pp.filter_cells">
                 <conditional name="filter">
@@ -177,8 +177,8 @@
             <when value="pp.highly_variable_genes">
                 <conditional name='flavor'>
                     <param argument="flavor" type="select" label="Flavor for computing normalized dispersion">
-                        <option value="seurat">seurat: expects non-logarithmized data</option>
-                        <option value="cell_ranger">cell_ranger: usually called for logarithmized data</option>
+                        <option value="seurat">Seurat</option>
+                        <option value="cell_ranger">Cell Ranger</option>
                     </param>
                     <when value="seurat">
                         <param argument="min_mean" type="float" value="0.0125" label="Minimal mean cutoff"/>
@@ -191,7 +191,7 @@
                     </when>
                 </conditional>
                 <param argument="n_bins" type="integer" value="20" label="Number of bins for binning the mean gene expression" help="Normalization is done with respect to each bin. If just a single gene falls into a bin, the normalized dispersion is artificially set to 1"/>
-                <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/>
+                <param argument="subset" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Inplace subset to highly-variable genes?" help="Otherwise it merely indicates highly variable genes."/>
             </when>
             <when value="pp.subsample">
                 <conditional name="type">
@@ -200,7 +200,7 @@
                         <option value="n_obs">By number of observation</option>
                     </param>
                     <when value="fraction">
-                        <param argument="fraction" type="float" value="" label="Subsample to this `fraction` of the number of observations"/>
+                        <param argument="fraction" type="float" value="" label="Subsample to this 'fraction' of the number of observations"/>
                     </when>
                     <when value="n_obs">
                         <param argument="n_obs" type="integer" min="0" value="" label="Subsample to this number of observations"/>
@@ -329,12 +329,14 @@
                     <param name="n_top_genes" value="2"/>
                 </conditional>
                 <param name="n_bins" value="20"/>
+                <param name="subset" value="true"/>
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="sc.pp.highly_variable_genes"/>
                 <has_text_matching expression="flavor='cell_ranger'"/>
                 <has_text_matching expression="n_top_genes=2"/>
                 <has_text_matching expression="n_bins=20"/>
+                <has_text_matching expression="subset=True"/>
             </assert_stdout>
             <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>