changeset 1:4ec52a83ec82 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c

--- a/inspect_and_manipulate.xml	Wed Sep 11 10:21:26 2024 +0000
+++ b/inspect_and_manipulate.xml	Tue Nov 05 11:55:01 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[
@@ -54,8 +55,8 @@
 
     #else if $method.inspect.inspect == 'Matrix'
         inspect<-LayerData(
-            seurat_obj, 
-            assay='$method.inspect.assay', 
+            seurat_obj,
+            assay='$method.inspect.assay',
             layer='$method.inspect.layer'
             )
         row.names = TRUE
@@ -672,7 +673,7 @@
 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.
 
@@ -717,7 +718,7 @@
 Merge
 =====
 
-Combine two Seurat Objects into a single Seurat Object. 
+Combine two Seurat Objects into a single Seurat Object.
 Each object will be placed in a separate layer, but you can choose to run the JoinLayers function after merging to combine the objects into a single layer.
 
 Subset
@@ -728,7 +729,7 @@
 DietSeurat
 ==========
 
-Keep only certain aspects of the Seurat object. 
+Keep only certain aspects of the Seurat object.
 Can be useful in functions that utilize merge as it reduces the amount of data in the merge
 
 More details on these essential commands can be found in the `seurat documentation
@@ -737,7 +738,7 @@
 AggregateExpression
 ===================
 
-Returns summed counts ("pseudobulk") for each identity class. 
+Returns summed counts ("pseudobulk") for each identity class.
 
 More details on the `seurat documentation
 <https://satijalab.org/seurat/reference/aggregateexpression>`__
@@ -746,7 +747,7 @@
 DefaultAssay
 ============
 
-Set the default assay for multimodal data. 
+Set the default assay for multimodal data.
 
 You can use the Inspect - General function to check which assay is currently active and which other assays are available.
 

--- a/macros.xml	Wed Sep 11 10:21:26 2024 +0000
+++ b/macros.xml	Tue Nov 05 11:55:01 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">