--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-find-markers.xml	Wed Apr 03 11:08:46 2019 -0400
@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1">
+  <description>to find differentially expressed genes between groups</description>
+  <macros>
+    <import>scanpy_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${input_obj_file}' input.h5 &&
+PYTHONIOENCODING=utf-8 scanpy-find-markers.py
+    -i input.h5
+    -f '${input_format}'
+    -o output.h5
+    -F '${output_format}'
+    -n '${n_genes}'
+    #if $output_markers
+        --output-text-file output.csv
+    #end if
+    #if $settings.default == "false"
+        -g '${settings.groupby}'
+        --reference '${settings.reference}'
+        --method '${settings.method}'
+        #if $settings.use_raw == "false"
+            --no-raw
+        #end if
+        #if $settings.rankby_abs
+            --rankby_abs
+        #end if
+        #if $settings.groups
+            --groups '${settings.groups}'
+        #end if
+#end if
+]]></command>
+
+  <inputs>
+    <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
+    <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
+    <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/>
+    <conditional name="settings">
+      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
+      <when value="true"/>
+      <when value="false">
+        <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
+        <param name="use_raw" type="boolean" checked="true" label="Use raw attribute if present"/>
+        <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"/>
+        <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="logreg">logistic regression</option>
+        </param>
+        <param name="rankby_abs" argument="--rankby_abs" type="boolean" 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."/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Marker object"/>
+    <data name="output_csv" format="csv" from_work_dir="output.csv" label="${tool.name} on ${on_string}: Marker table">
+      <filter>output_markers</filter>
+    </data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input_obj_file" value="find_cluster.h5"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="output_csv" value="true"/>
+      <param name="n_genes" value="50"/>
+      <param name="output_markers" value="false"/>
+      <param name="default" value="false"/>
+      <param name="groupby" value="louvain"/>
+      <param name="method" value="t-test_overestim_var"/>
+      <param name="rankby_abs" value="false"/>
+      <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+=============================================================
+Rank genes for characterizing groups (`tl.rank_genes_groups`)
+=============================================================
+
+Rank genes for characterizing groups.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>