changeset 17:f04dd4e5b6a7 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit a49eda957d6c894fee1514c9df649444966691ce-dirty"

--- a/scanpy-find-markers.xml	Wed Oct 07 16:06:38 2020 +0000
+++ b/scanpy-find-markers.xml	Thu Oct 15 16:06:41 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -12,7 +12,13 @@
     --save diffexp.tsv
 #end if
     --n-genes '${n_genes}'
-#set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
+#if $groupby_file
+    #set f = open($groupby_file.__str__)
+    #set groupby = f.read().strip()
+    #silent f.close
+#else
+    #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
+#end if
     --groupby '${groupby}'
 #if $settings.default == "false"
     #if $settings.key_added
@@ -39,6 +45,8 @@
     <param name="output_markers" type="boolean" checked="true" label="Output markers table in tsv format"/>
     <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
     <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
+    <param name="groupby_file" argument="--groupby" type="data" format="txt,tsv" optional="true"
+        label="File with groupby. Overrides the groupby setting"/>
     <conditional name="settings">
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>
@@ -92,6 +100,21 @@
       <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
       <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
     </test>
+    <test>
+      <param name="input_obj_file" value="louvain_1.0"/>
+      <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
+      <param name="output_tsv" value="true"/>
+      <param name="n_genes" value="50"/>
+      <param name="output_markers" value="true"/>
+      <param name="default" value="false"/>
+      <param name="groupby_file" value="groupby.txt"/>
+      <param name="key_added" value="GROUPBY_marker"/>
+      <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"/>
+      <output name="output_tsv" file="diffexp.tsv" ftype="tabular" compare="sim_size"/>
+    </test>
   </tests>
 
   <help><![CDATA[