changeset 1:74fa68f4e579 draft default tip

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

--- a/integrate.xml	Wed Sep 11 10:20:51 2024 +0000
+++ b/integrate.xml	Tue Nov 05 11:55:09 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[
@@ -15,7 +16,7 @@
 
 #if $method.method == 'SplitLayers'
     seurat_obj[['$method.assay']]<-split(
-        seurat_obj[['$method.assay']], 
+        seurat_obj[['$method.assay']],
         f = seurat_obj[['$method.factor', drop = TRUE]]
     )
 
@@ -26,12 +27,12 @@
     #end if
 
     seurat_obj<-IntegrateLayers(
-        seurat_obj, 
+        seurat_obj,
         method = $method.integration.integration_method,
         #if $method.integration.integration_method == 'CCAIntegration'
             #if $method.integration.adv.k_filter
             k.filter = $method.integration.adv.k_filter,
-            #else           
+            #else
             k.filter = NA,
             #end if
             dims = 1:$method.integration.adv.dims,
@@ -73,7 +74,7 @@
         #else if $method.integration.integration_method == 'RPCAIntegration'
             #if $method.integration.adv.k_filter
             k.filter = $method.integration.adv.k_filter,
-            #else           
+            #else
             k.filter = NA,
             #end if
             dims = 1:$method.integration.adv.dims,
@@ -87,7 +88,7 @@
             sd.weight = $method.integration.adv.sd_weight,
             preserve.order = $method.integration.adv.preserve_order,
         #end if
-        orig.reduction = '$method.orig_reduction', 
+        orig.reduction = '$method.orig_reduction',
         new.reduction = '$method.new_reduction',
         #if $method.assay != ''
         assay = '$method.assay',
@@ -219,7 +220,7 @@
             <conditional name="method">
                 <param name="method" value="SplitLayers"/>
                 <param name="assay" value="RNA"/>
-                <param name="factor" value="Group"/>                 
+                <param name="factor" value="Group"/>
             </conditional>
             <section name="advanced_common">
                 <param name="show_log" value="true"/>
@@ -261,7 +262,7 @@
                     <param name="integration_method" value="HarmonyIntegration"/>
                 </conditional>
                 <param name="orig_reduction" value="pca"/>
-                <param name="new_reduction" value="integrated.harm"/>            
+                <param name="new_reduction" value="integrated.harm"/>
             </conditional>
             <section name="advanced_common">
                 <param name="show_log" value="true"/>
@@ -310,7 +311,7 @@
 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.
 
@@ -327,7 +328,7 @@
 Integrate
 =========
 
-Multiple layers are integrated to enable them to be analysed together. 
+Multiple layers are integrated to enable them to be analysed together.
 
 Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI.
 
@@ -345,7 +346,7 @@
 PrepSCTFindMarkers
 ==================
 
-Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate. 
+Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate.
 The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts.
 
 More details on the `seurat documentation

--- a/macros.xml	Wed Sep 11 10:20:51 2024 +0000
+++ b/macros.xml	Tue Nov 05 11:55:09 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">