# HG changeset patch
# User iuc
# Date 1643920864 0
# Node ID 2a9baa0c43168a96be27e6208e6a0ebf2018581b
# Parent  83ead2be47b21be586f33838e96d9bd8eab3e9f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"

diff -r 83ead2be47b2 -r 2a9baa0c4316 shovill.xml
--- a/shovill.xml	Thu Jul 02 08:58:03 2020 -0400
+++ b/shovill.xml	Thu Feb 03 20:41:04 2022 +0000
@@ -1,5 +1,8 @@
-<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0">
+<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1">
     <description>Faster SPAdes assembly of Illumina reads</description>
+    <xrefs>
+        <xref type="bio.tools">shovill</xref>
+    </xrefs>
     <macros>
         <token name="@TOOL_VERSION@">1.1.0</token>
     </macros>
@@ -8,16 +11,29 @@
     </requirements>
     <version_command>shovill --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+    ## NOTE: the wrapper uses cp instead of ln -s because of this problem
+    ## with shovill 1.1.0: https://github.com/tseemann/shovill/issues/157
+
         #if str($library.lib_type) == "paired"
             #set r1_ext = $library.R1.extension
             #set r2_ext = $library.R2.extension
-            ln -s '$library.R1' fastq_r1.'$r1_ext' &&
-            ln -s '$library.R2' fastq_r2.'$r2_ext' && 
+            #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2'
+                cp '$library.R1' fastq_r1.'$r1_ext' &&
+                cp '$library.R2' fastq_r2.'$r2_ext' && 
+            #else
+                ln -s '$library.R1' fastq_r1.'$r1_ext' &&
+                ln -s '$library.R2' fastq_r2.'$r2_ext' && 
+            #end if
         #else if str($library.lib_type) == "collection"
             #set r1_ext = $library.input1.forward.extension
             #set r2_ext = $library.input1.reverse.extension
-            ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
-            ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
+            #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2'
+                cp '$library.input1.forward' fastq_r1.'$r1_ext' &&
+                cp '$library.input1.reverse' fastq_r2.'$r2_ext' &&
+            #else
+                ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
+                ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
+            #end if
         #end if
 
 	## Sets the memory used by Shovill according to the following conditions
@@ -209,8 +225,8 @@
         </test>
         <test> <!-- Test 6: Gzipped input with trimming -->
             <param name="lib_type" value="paired" />
-            <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" />
-            <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" />
+            <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" />
             <param name="trim" value="true" />
             <output name="contigs" ftype="fasta">
                 <assert_contents>