# HG changeset patch
# User iuc
# Date 1740999978 0
# Node ID dada2881d772c3be3b3b0d5cbf6a0d9caff98819
# Parent  2463908405d39d44c72e2428f2dbea51a31c6909
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390

diff -r 2463908405d3 -r dada2881d772 macros.xml
--- a/macros.xml	Tue Aug 23 07:55:55 2022 +0000
+++ b/macros.xml	Mon Mar 03 11:06:18 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.15.4</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">3.15.5</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
@@ -148,6 +148,7 @@
 <token name="@RESOURCES@"><![CDATA[
 -t \${GALAXY_SLOTS:-4}
 -m \$((\${GALAXY_MEMORY_MB:-8192}/1024))
+--tmp-dir \${TMPDIR}	
 ]]></token>
 
 <token name="@INPUT_READS_MAIN@"><![CDATA[
@@ -384,16 +385,16 @@
 
 <token name="@STATS@"><![CDATA[
 #if 'cs' in $optional_output
-    && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.'
+    && (test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.')
 #end if
 #if 'ss' in $optional_output
-    && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.'
+    && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.')
 #end if
 ]]></token>
 
 <token name="@CORRECTED@"><![CDATA[
     #if 'corrected' in $optional_output
-        && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.'
+        && (test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.')
     #end if
 ]]></token>
 
@@ -504,10 +505,6 @@
             </param>
             <when value="true">
                 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
-                <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
-                    <option value="true" selected="true">True</option>
-                    <option value="false">False</option>
-                </param>
             </when>
             <when value="false"/>
         </conditional>
diff -r 2463908405d3 -r dada2881d772 metaspades.xml
--- a/metaspades.xml	Tue Aug 23 07:55:55 2022 +0000
+++ b/metaspades.xml	Mon Mar 03 11:06:18 2025 +0000
@@ -3,6 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">metaspades</xref>
+    </xrefs>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
@@ -41,9 +44,6 @@
         <section name="arf" title="Additional read files">
             <expand macro="nanopore_pacbio"/>
         </section>
-        <section name="arf" title="Additional read files">
-            <expand macro="nanopore_pacbio"/>
-        </section>
         <expand macro="kmer"/>
         <expand macro="phred"/>
         <expand macro="pipeline_options">