--- a/remove_confounders.xml	Thu Dec 05 07:11:58 2019 -0500
+++ b/remove_confounders.xml	Thu Dec 12 09:26:22 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="scanpy_remove_confounders" name="Remove confounders" version="@version@" profile="@profile@">
+<tool id="scanpy_remove_confounders" name="Remove confounders" version="@galaxy_version@" profile="@profile@">
     <description>with scanpy</description>
     <macros>
         <import>macros.xml</import>
@@ -67,16 +67,16 @@
         <expand macro="inputs_anndata"/>
         <conditional name="method">
             <param argument="method" type="select" label="Method used for plotting">
-                <option value="pp.regress_out">Regress out unwanted sources of variation, using `pp.regress_out`</option>
-                <option value="pp.mnn_correct">Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct`</option>
-                <option value="pp.combat">Correct batch effects with ComBat function, using `pp.combat`</option>
+                <option value="pp.regress_out">Regress out unwanted sources of variation, using 'pp.regress_out'</option>
+                <option value="pp.mnn_correct">Correct batch effects by matching mutual nearest neighbors, using 'pp.mnn_correct'</option>
+                <option value="pp.combat">Correct batch effects with ComBat function, using 'pp.combat'</option>
             </param>
             <when value="pp.regress_out">
                 <param argument="keys" type="text" value="" label="Keys for observation annotation on which to regress on" help="Keys separated by a comma"/>
             </when>
             <when value="pp.mnn_correct">
                 <param name="extra_adata" type="data" multiple="true" optional="true" format="h5ad" label="Extra annotated data matrix" help="They should have same number of variables."/>
-                <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from `.var_names`. If not set, all vars are used"/>
+                <param argument="var_subset" type="text" value="" optional="true" label="The subset of vars to be used when performing MNN correction" help="List of comma-separated key from '.var_names'. If not set, all vars are used"/>
                 <param argument="batch_key" type="text" value="batch" label="Batch key for the concatenate"/>
                 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">
                     <option value="-">-</option>