# HG changeset patch
# User ebi-gxa
# Date 1676554129 0
# Node ID 81c34e67f262985d3f4a54c19aeb74dd65e2830c
# Parent  eb01a7e59e9a515ecd750e06c857e43cceea5738
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty

diff -r eb01a7e59e9a -r 81c34e67f262 scanpy-find-markers.xml
--- a/scanpy-find-markers.xml	Thu Oct 28 10:04:02 2021 +0000
+++ b/scanpy-find-markers.xml	Thu Feb 16 13:28:49 2023 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -97,7 +97,6 @@
       <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"/>
@@ -111,8 +110,7 @@
     <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="output_format" value="no_matrix_output"/>
       <param name="n_genes" value="50"/>
       <param name="output_markers" value="true"/>
       <param name="default" value="false"/>
@@ -120,7 +118,6 @@
       <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>
diff -r eb01a7e59e9a -r 81c34e67f262 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Thu Oct 28 10:04:02 2021 +0000
+++ b/scanpy_macros2.xml	Thu Feb 16 13:28:49 2023 +0000
@@ -1,9 +1,11 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.8.1+3</token>
+  <token name="@TOOL_VERSION@">1.8.1</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
   <token name="@PROFILE@">18.01</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
+adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.
 
 1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.
 
@@ -99,18 +101,20 @@
   </xml>
 
   <xml name="output_object_params">
-    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
+    <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="AnnData or Loom. Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
       <option value="anndata_h5ad" selected="true">AnnData format</option>
       <option value="anndata">AnnData format (h5 for older versions)</option>
       <option value="loom">Loom format</option>
       <option value="loom_legacy">Loom format (h5 for older versions)</option>
+      <option value="no_matrix_output">No packaged matrix output</option>
     </param>
   </xml>
 
   <xml name="output_object_params_no_loom">
-    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
+    <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
       <option value="anndata_h5ad" selected="true">AnnData format</option>
       <option value="anndata">AnnData format (h5 for older versions)</option>
+      <option value="no_matrix_output">No packaged matrix output (useful for cases where auxiliary files are generated)</option>
     </param>
   </xml>
 
@@ -118,7 +122,7 @@
     <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
       <filter>output_format == 'anndata_h5ad'</filter>
     </data>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
       <filter>output_format == 'anndata'</filter>
     </data>
   </xml>
@@ -127,13 +131,13 @@
     <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
       <filter>output_format == 'anndata_h5ad'</filter>
     </data>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
       <filter>output_format == 'anndata'</filter>
     </data>
     <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
       <filter>output_format == 'loom_legacy'</filter>
     </data>
-    <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
+    <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom (h5)">
       <filter>output_format == 'loom'</filter>
     </data>
   </xml>