diff seurat_convert.xml @ 1:834f7d8e5b4c draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6

--- a/seurat_convert.xml	Fri Mar 04 07:28:21 2022 +0000
+++ b/seurat_convert.xml	Sat Mar 02 10:42:13 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="seurat_convert" name="Seurat 3 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
+<tool id="seurat_convert" name="Seurat 4 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
     <description>translates different single cell formats</description>
     <macros>
         <import>seurat_macros.xml</import>
@@ -6,6 +6,7 @@
     <expand macro="requirements" />
     <expand macro="version" />
     <command detect_errors="exit_code"><![CDATA[
+@INPUT_OBJ_PREAMBLE@
 seurat-convert.R
 @INPUT_OBJECT@
 @OUTPUT_OBJECT@
@@ -76,33 +77,47 @@
           <param name="format" value="rds_seurat"/>
           <output name="rds_seurat_file">
             <assert_contents>
-              <has_size value="2965562" delta="200000"/>
+              <has_size value="3761959" delta="200000"/>
             </assert_contents>
           </output>
         </test>
+        <!-- <test>
+          <conditional name="input">
+            <param name="format" value="anndata"/>
+            <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells_sc182.h5ad" ftype="h5ad"/>
+          </conditional>
+          <param name="format" value="rds_seurat"/>
+          <output name="rds_seurat_file">
+            <assert_contents>
+              <has_size value="3761959" delta="200000"/>
+            </assert_contents>
+          </output>
+        </test> -->
+
     </tests>
     <help><![CDATA[
 .. class:: infomark
 
 **What it does**
 
-This tool uses Seurat 3 to convert formats. Possible inputs are:
+@SEURAT_INTRO@
+
+This tool uses Seurat 4 to convert formats. Possible inputs are:
 
-    * Seurat 3
-    * Loom (probably earlier than Loom 3.0)
-    * AnnData (contemporary versions to Seurat 3, most likely up to AnnData 0.6.22.post1)
+    * Seurat 3/4
+    * Loom (versions contemporary to Seurat 4)
+    * AnnData (contemporary versions to Seurat 4)
     * Single Cell Experiment
 
 Possible outputs are:
 
-    * Seurat 3
-    * Loom (as produced by loomR package)
+
+    * Seurat 4
+    * Loom
     * Single Cell Experiment
 
 For newer versions of AnnData and Loom, please try the Seurat 4 version of this tool.
 
-@SEURAT_INTRO@
-
 
 .. _Seurat: https://www.nature.com/articles/nbt.4096
 .. _Satija Lab: https://satijalab.org/seurat/