# HG changeset patch
# User iuc
# Date 1740999938 0
# Node ID c78e8c156c264d87fcb96fcc496b77481e5c3e07
# Parent  6da6a414803fc60a91c6302b1b03ce73f2f516da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390

diff -r 6da6a414803f -r c78e8c156c26 macros.xml
--- a/macros.xml	Tue Aug 23 07:52:57 2022 +0000
+++ b/macros.xml	Mon Mar 03 11:05:38 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 6da6a414803f -r c78e8c156c26 spades.xml
--- a/spades.xml	Tue Aug 23 07:52:57 2022 +0000
+++ b/spades.xml	Mon Mar 03 11:05:38 2025 +0000
@@ -1,8 +1,11 @@
-<tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <description>genome assembler for genomes of regular and single-cell projects</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">spades</xref>
+    </xrefs>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <expand macro="version_command"/>