# HG changeset patch
# User iuc
# Date 1760632919 0
# Node ID e783c7734e044731d1db8afc1d79398cc74a9e4e
# Parent  0884581dc9696a2f2c42f9828a54e3f56fa3e878
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash commit ff9564c2e6924fab084b6e02a3a196650041636a

diff -r 0884581dc969 -r e783c7734e04 mash_sketch.xml
--- a/mash_sketch.xml	Tue Sep 23 13:47:54 2025 +0000
+++ b/mash_sketch.xml	Thu Oct 16 16:41:59 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
     <description>Create a reduced sequence representation based on min-hashes</description>
     <macros>
         <import>macros.xml</import>
@@ -8,20 +8,24 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
     
+        #import re
         #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}" &&
+                    #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.reads_input.reads_1.element_identifier)
+                    cat '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2' > '$safe_file_name'  &&
                 #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}" &&
+                    #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.reads_input.reads.element_identifier)
+                    echo $no_extension && 
+                    cat '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse' > '$safe_file_name' &&
                 #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}" &&
+                    #set safe_file_name = re.sub(r'[^\w\-_\.]', '_', $reads_assembly.reads_input.reads.element_identifier)
+                    ln -s '$reads_assembly.reads_input.reads'  '$safe_file_name' &&
                 #end if
         #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly":
-            ln -s '${reads_assembly.assembly}' "${reads_assembly.assembly.element_identifier}" &&
+            #set safe_file_name  =   re.sub(r'[^\w\-_\.]', '_', $reads_assembly.assembly.element_identifier)
+            ln -s '${reads_assembly.assembly}' '$safe_file_name'  &&
         #end if
 
         mash sketch
@@ -37,20 +41,11 @@
                 #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.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.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.element_identifier}"
-                #end if
             #elif str( $reads_assembly.reads_assembly_selector ) == "assembly":
                 -p \${GALAXY_SLOTS:-1}
                 ${reads_assembly.individual_sequences}
-                "${reads_assembly.assembly.element_identifier}"
             #end if
+            '$safe_file_name'
             -o 'sketch'
     ]]></command>
     <inputs>
@@ -177,6 +172,18 @@
             </conditional>
             <output name="sketch" file="test_07_mash_sketch.msh" compare="sim_size" />
         </test>
+        <test expect_num_outputs="1">
+            <conditional name="reads_assembly">
+                <param name="reads_assembly_selector" value="reads"/>
+                <conditional name="reads_input">
+                    <param name="reads_input_selector" value="paired"/>
+                    <param name="reads_1" value="L1_R1.fastqsanger.gz"/>
+                    <param name="reads_2" value="L1_R2.fastqsanger.gz"/>
+                </conditional>
+                <param name="minimum_kmer_copies" value="2"/>
+            </conditional>
+            <output name="sketch" file="test_08_mash_sketch.msh" compare="sim_size" />
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r 0884581dc969 -r e783c7734e04 test-data/L1_R1.fastqsanger.gz
Binary file test-data/L1_R1.fastqsanger.gz has changed
diff -r 0884581dc969 -r e783c7734e04 test-data/L1_R2.fastqsanger.gz
Binary file test-data/L1_R2.fastqsanger.gz has changed
diff -r 0884581dc969 -r e783c7734e04 test-data/test_08_mash_sketch.msh
Binary file test-data/test_08_mash_sketch.msh has changed