# HG changeset patch
# User iuc
# Date 1651169494 0
# Node ID 9cd178127b1953bab31ef04f78c65dc9789aaabb
# Parent  eadfd71dde3790fc1b82d3393f839103e66fdcbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f09759ed13dd6c6efabbdd79fb171b2d3bfdc927"

diff -r eadfd71dde37 -r 9cd178127b19 macros.xml
--- a/macros.xml	Tue Oct 05 15:58:14 2021 +0000
+++ b/macros.xml	Thu Apr 28 18:11:34 2022 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
-    <token name="@SUFFIX_VERSION@">4</token>
+    <token name="@SUFFIX_VERSION@">5</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0196</edam_topic>
diff -r eadfd71dde37 -r 9cd178127b19 meryl.xml
--- a/meryl.xml	Tue Oct 05 15:58:14 2021 +0000
+++ b/meryl.xml	Thu Apr 28 18:11:34 2022 +0000
@@ -77,18 +77,21 @@
                 #set size=$operation_type.options_kmer_size.input_kmer_size
             #end if
             #for $i, $read in enumerate($paternal_reads):
-                mkdir 'paternal{$i}.meryl' &&
-                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
+                mkdir 'paternal${i}.meryl' &&
+                ln -s '$read' ./input_paternal_${i}.${read.ext} &&
+                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_paternal_${i}.${read.ext} output 'paternal${i}.meryl' &&
             #end for
             meryl union-sum paternal*.meryl output pat.meryl &&
             #for $i, $read in enumerate($maternal_reads):
-                mkdir 'maternal{$i}.meryl' &&
-                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
+                mkdir 'maternal${i}.meryl' &&
+                ln -s '$read' ./input_maternal_${i}.${read.ext} &&
+                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_maternal_${i}.${read.ext} output 'maternal${i}.meryl' &&
             #end for
             meryl union-sum maternal*.meryl output mat.meryl &&
             #for $i, $read in enumerate($child_reads):
-                mkdir 'child{$i}.meryl' &&
-                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
+                mkdir 'child${i}.meryl' &&
+                ln -s '$read' ./input_child_${i}.${read.ext} &&
+                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
             #end for
             meryl union-sum child*.meryl output child.meryl &&
             ## mat specific kmers