# HG changeset patch
# User iuc
# Date 1752824712 0
# Node ID f66590d0d3afd92932824318a3088269c5ac5982
# Parent  90e95e9ee1900108465860e742b2df7c9523300b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit b12efa10c543d2783274da8b47853297c8255906

diff -r 90e95e9ee190 -r f66590d0d3af macros.xml
--- a/macros.xml	Wed Dec 20 18:03:30 2023 +0000
+++ b/macros.xml	Fri Jul 18 07:45:12 2025 +0000
@@ -11,7 +11,11 @@
     -o "."
     -e "output"
     ]]></token>
-    
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">velocyto</xref>
+        </xrefs>
+    </xml>
     <xml name="bcffile" >
         <param argument="-b" type="data" format="tabular,txt" optional="true"
                label="Barcodes file to filter BAM"
@@ -53,4 +57,4 @@
             <requirement type="package" version="@VERSION@" >velocyto.py</requirement>
         </requirements>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r 90e95e9ee190 -r f66590d0d3af velocyto_cli.xml
--- a/velocyto_cli.xml	Wed Dec 20 18:03:30 2023 +0000
+++ b/velocyto_cli.xml	Fri Jul 18 07:45:12 2025 +0000
@@ -1,9 +1,10 @@
-<tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy2">
+<tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy3">
     <description>pre-process data for the analysis of RNA velocity</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="edam"/>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <stdio>
       <!-- Anything other than zero is an error -->
@@ -48,7 +49,7 @@
     -b '$main.b'
   #end if
   #if str($main.m) != 'None':
-    -m '$main.m' 
+    -m '$main.m'
   #end if
   $main.c
   $main.U
@@ -68,7 +69,7 @@
     -s '$main.s'
   #end if
   #if str($main.m) != 'None':
-    -m '$main.m' 
+    -m '$main.m'
   #end if
   $main.M
   -t '$main.t'
@@ -82,7 +83,7 @@
 run-smartseq2
    @LOOMOUT@
   #if str($main.m) != 'None':
-    -m '$main.m' 
+    -m '$main.m'
   #end if
   -t '$main.t'
   @SAMTOOLS_OPTS@
@@ -97,7 +98,7 @@
     -b '$main.b'
   #end if
   #if str($main.m) != 'None':
-    -m '$main.m' 
+    -m '$main.m'
   #end if
   -t '$main.t'
   @SAMTOOLS_OPTS@
@@ -185,7 +186,7 @@
                 <expand macro="loomdtype" token_16_selected="false" token_32_selected="true" />
             </when>
             <when value="dropest-bc-correct" >
-                <param name="bamfile" type="data" format="BAM"
+                <param name="bamfile" type="data" format="bam"
                        label="Bam file with sorted reads obtained from DropEst" />
                 <param name="rfile" type="data" format="rds"
                        label="R dump RDS file generated from DropEst" />