# HG changeset patch
# User iuc
# Date 1730807692 0
# Node ID 6bccf5f85f9229a61a4eddf111a8ab1b287ddd23
# Parent  c3170652bd98c499c1bbc85a175564fbaf373e5e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c

diff -r c3170652bd98 -r 6bccf5f85f92 macros.xml
--- a/macros.xml	Wed Sep 11 10:20:38 2024 +0000
+++ b/macros.xml	Tue Nov 05 11:54:52 2024 +0000
@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">5.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">23.0</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">seurat</xref>
+        </xrefs>
+      </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
@@ -141,7 +146,7 @@
         </data>
     </xml>
     <token name="@CMD_inspect_rds_outputs@"><![CDATA[
-write.table(inspect, 'inspect_out.tab', sep="\t", col.names = col.names, row.names = row.names, quote = FALSE)    
+write.table(inspect, 'inspect_out.tab', sep="\t", col.names = col.names, row.names = row.names, quote = FALSE)
     ]]>
     </token>
     <xml name="plot_out">
diff -r c3170652bd98 -r 6bccf5f85f92 normalize_select_features_scale.xml
--- a/normalize_select_features_scale.xml	Wed Sep 11 10:20:38 2024 +0000
+++ b/normalize_select_features_scale.xml	Tue Nov 05 11:54:52 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -404,7 +405,7 @@
 Seurat
 ======
 
-Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 
+Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
 
 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
 
@@ -444,7 +445,7 @@
 Scale and regress the data with ScaleData
 =========================================
 
-Scale and center features in the dataset. 
+Scale and center features in the dataset.
 
 If variables are provided in vars.to.regress, they are individually regressed against each feature, and the resulting residuals are then scaled and centered.
 
@@ -454,7 +455,7 @@
 SCTransform
 ===========
 
-Use this function as an alternative to the NormalizeData, FindVariableFeatures, ScaleData workflow. 
+Use this function as an alternative to the NormalizeData, FindVariableFeatures, ScaleData workflow.
 
 Results are saved in a new assay (named SCT by default) with counts being (corrected) counts, data being log1p(counts), scale.data being pearson residuals; sctransform::vst intermediate results are saved in misc slot of new assay.