# HG changeset patch
# User ebi-gxa
# Date 1676554158 0
# Node ID b8126b3bf5d04c1d600d6a30419f08e3abeafefc
# Parent  8ca3ab8300ceaa4e10d5b17d9a8cabb6dbf3ce90
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 8ca3ab8300ce -r b8126b3bf5d0 scanpy-multiplet-scrublet.xml
--- a/scanpy-multiplet-scrublet.xml	Thu Oct 28 10:03:41 2021 +0000
+++ b/scanpy-multiplet-scrublet.xml	Thu Feb 16 13:29:18 2023 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
   <description>remove multiplets from annData objects with Scrublet</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -13,6 +13,8 @@
 #end if
 #if $batch_key
   --batch-key '${batch_key}'
+#else if $sample_key
+  --batch-key '${sample_key}'
 #end if  
 $filter
 #if $settings.default == "false"
@@ -39,7 +41,8 @@
     <param name="threshold" argument="--threshold" type="float" optional="true" label="Doublet score threshold." help="Threshold for calling a transcriptome a doublet. If not set, this is set automatically by looking for the minimum between the two modes of the doublet_scores_sim_ histogram. It is best  practice to check the threshold visually using the doublet_scores_sim_ histogram and/or based on co-localization of predicted doublets in a 2-D embedding."/>
     <param name="filter" argument="--filter" type="boolean" truevalue="--filter" falsevalue="" checked="False"
          label="Remove predicted multiplets?" help="By default, the output object is annotated but not filtered according to the scrublet status."/>
-     <param name="batch_key" type="text" argument="--batch-key" optional="true" label="Where batches are present, the name of the column in adata.obs that differentiates among experiments/batches."/>
+    <param name="batch_key" type="text" argument="--batch-key" optional="true" label="Where batches are present, the name of the column in adata.obs that differentiates among experiments/batches."/>
+    <param name="sample_key" type="text" argument="--batch-key" optional="true" label="The name of the column in adata.obs that differentiates among samples. This is a convenience for workflows, this is overriden if the batch key is set. It is an Scrubblet best practice to operate per samples rather than on the complete dataset (and it should use less memory)."/>
     <conditional name="settings">
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>
diff -r 8ca3ab8300ce -r b8126b3bf5d0 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Thu Oct 28 10:03:41 2021 +0000
+++ b/scanpy_macros2.xml	Thu Feb 16 13:29:18 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>