# HG changeset patch
# User iuc
# Date 1758635317 0
# Node ID 3852f36e3154cfd6cfaba282e21e73e340b99e88
# Parent  c73c3dfe1af8b6371a31f0766bd725fbd024e26d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 16d60f67e8fef6c51af1161d677c32d37cb0cab2

diff -r c73c3dfe1af8 -r 3852f36e3154 mash_sketch.xml
--- a/mash_sketch.xml	Thu Sep 11 10:22:17 2025 +0000
+++ b/mash_sketch.xml	Tue Sep 23 13:48:37 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>Create a reduced sequence representation based on min-hashes</description>
     <macros>
         <import>macros.xml</import>
@@ -7,32 +7,49 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
+    
+        #if str ( $reads_assembly.reads_assembly_selector ) == "reads":
+                #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired":
+                    ln -s '$reads_assembly.reads_input.reads_1' "${reads_assembly.reads_input.reads_1.element_identifier}" &&
+                    ln -s '$reads_assembly.reads_input.reads_2' "${reads_assembly.reads_input.reads_1.element_identifier}" &&
+                #end if
+                #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection":
+                    ln -s '$reads_assembly.reads_input.reads.forward' "${reads_assembly.reads_input.reads.forward.element_identifier}" &&
+                    ln -s '$reads_assembly.reads_input.reads.reverse' "${reads_assembly.reads_input.reads.reverse.element_identifier}" &&
+                #end if
+                #if str( $reads_assembly.reads_input.reads_input_selector ) == "single":
+                    ln -s '$reads_assembly.reads_input.reads' "${reads_assembly.reads_input.reads.element_identifier}" &&
+                #end if
+        #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly":
+            ln -s '${reads_assembly.assembly}' "${reads_assembly.assembly.element_identifier}" &&
+        #end if
+
         mash sketch
             -s '${sketch_size}'
             -k '${kmer_size}'
             -w '${prob_threshold}'
-            #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
+            #if str( $reads_assembly.reads_assembly_selector ) == "reads":
                 -m '${reads_assembly.minimum_kmer_copies}'
                 -r
-                #if $reads_assembly.target_coverage
+                #if $reads_assembly.target_coverage :
                     -c '${reads_assembly.target_coverage}'
                 #end if
-                #if $reads_assembly.genome_size
+                #if $reads_assembly.genome_size :
                     -g '${reads_assembly.genome_size}'
                 #end if
-                #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
-                    '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2'
+                #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired" :
+                    "${reads_assembly.reads_input.reads_1.element_identifier}" "${reads_assembly.reads_input.reads_1.element_identifier}}"
                 #end if
-                #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
-                    '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
+                #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection":
+                    "${reads_assembly.reads_input.reads.forward.element_identifier}" "${reads_assembly.reads_input.reads.reverse.element_identifier}"
                 #end if
-                #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
-                    '$reads_assembly.reads_input.reads'
+                #if str( $reads_assembly.reads_input.reads_input_selector ) == "single":
+                    "${reads_assembly.reads_input.reads.element_identifier}"
                 #end if
-            #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
+            #elif str( $reads_assembly.reads_assembly_selector ) == "assembly":
                 -p \${GALAXY_SLOTS:-1}
-                '${assembly}'
                 ${reads_assembly.individual_sequences}
+                "${reads_assembly.assembly.element_identifier}"
             #end if
             -o 'sketch'
     ]]></command>
diff -r c73c3dfe1af8 -r 3852f36e3154 test-data/res_paste.msh
Binary file test-data/res_paste.msh has changed