--- a/scanpy-find-markers.xml	Thu Feb 16 13:28:49 2023 +0000
+++ b/scanpy-find-markers.xml	Sat Jul 15 08:44:51 2023 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy91" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -26,7 +26,6 @@
         --key-added '${key_added}'
     #end if
     --method '${settings.method}'
-    ${settings.use_raw}
     ${settings.rankby_abs}
     #if $settings.groups
         --groups '${settings.groups}'
@@ -35,6 +34,12 @@
     #if $settings.filter.default == "false"
       --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}'
     #end if
+    #if $settings.layer
+        --layer '${settings.layer}'
+        --no-raw
+    #else
+        ${settings.use_raw}
+    #end if
     $settings.pts $settings.tie_correct
     #end if
     @INPUT_OPTS@
@@ -58,14 +63,16 @@
         <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
           <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
           <option value="t-test">t-test</option>
-          <option value="wilcoxon">wilcoxon test, currently broken don't use</option>
+          <option value="wilcoxon">wilcoxon test</option>
           <option value="logreg">logistic regression</option>
         </param>
         <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true"
-               label="Use raw attribute if present"/>
+               label="Use raw attribute if present" help="Uses adata.raw, usually what was available before processing. If the layer option is set, this will be ignored (raw will not be used)."/>
         <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false"
                label="Rank by absolute value of the scores instead of the scores"/>
-        <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/>
+        <param name="groups" argument="--groups" optional="true" type="text"
+               label="Subset of groups/clusters to which comparisons should be restricted" 
+               help="Comma separated list of groups existing within the groupby field in obs. Currently it fails if a single group is given, provide at least two."/>
         <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/>
         <conditional name="filter">
           <param name="default" type="boolean" checked="false" label="Use filtering defaults"/>
@@ -79,6 +86,8 @@
                    help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
           </when>
         </conditional>
+        <param name="layer" argument="--layer" type="text" optional="true" label="Layer to use for marker genes computation" 
+                help="The method prefers matrices/layers that are logged. Leave empty to use the default .X matrix. It will override the use of raw if set."/>
         <param name="pts" argument="--pts"  type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
         <param name="tie_correct" argument="--tie-correct"  type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/>
       </when>
@@ -120,6 +129,22 @@
       <param name="rankby_abs" value="false"/>
       <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
     </test>
+    <test>
+      <param name="input_obj_file" value="mnn.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="n_genes" value="50"/>
+      <param name="output_markers" value="true"/>
+      <param name="default" value="false"/>
+      <param name="groupby" value="louvain"/>
+      <param name="key_added" value="l_markers"/>
+      <param name="method" value="wilcoxon"/>
+      <param name="layer" value="mnn"/>
+      <output name="output_h5ad" ftype="h5ad">
+        <assert_contents>
+          <has_h5_keys keys="uns/l_markers_mnn"/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
 
   <help><![CDATA[