changeset 4:8ca3ab8300ce draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9ea121884e1aecd2ee66a0686057cb3ed904b9eb-dirty"
author ebi-gxa
date Thu, 28 Oct 2021 10:03:41 +0000
parents 0c70a41fce6f
children
files scanpy-multiplet-scrublet.xml scanpy_macros2.xml
diffstat 2 files changed, 8 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/scanpy-multiplet-scrublet.xml	Fri Oct 15 15:05:00 2021 +0000
+++ b/scanpy-multiplet-scrublet.xml	Thu Oct 28 10:03:41 2021 +0000
@@ -113,6 +113,10 @@
 
     This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/docsearch/external/scanpy.external.pp.scrublet.html.
 
+    **Note**
+
+    Where a threshold is not provided, Scrublet will try to automatically set one based on simulations, but this does not always work. There will be a warning, and no 'threshold' slot will be populated in .uns['scrublet']. The 'predicted_doublets' slot in .obs will be set to False for all cells such that no filtering will occur if this column is supplied to filtering steps. You can use the 'Scanpy Plot Scrublet' tool to plot the distribution of scores yourself and estimate a threshold to override this behaviour. 
+
     @HELP@
 
     @VERSION_HISTORY@
--- a/scanpy_macros2.xml	Fri Oct 15 15:05:00 2021 +0000
+++ b/scanpy_macros2.xml	Thu Oct 28 10:03:41 2021 +0000
@@ -1,10 +1,12 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.8.1+2</token>
+  <token name="@TOOL_VERSION@">1.8.1+3</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+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.
+
 1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.
 
 1.8.1+1+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.
@@ -65,7 +67,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.1.2">scanpy-scripts</requirement>
+      <requirement type="package" version="1.1.3">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>