--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spades_cpu7mem28.xml	Fri Mar 13 12:21:18 2026 +0000
@@ -0,0 +1,85 @@
+<tool id="spades_cpu7mem28" 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"/>
+    <command detect_errors="exit_code"><![CDATA[
+
+#set $library = 1
+
+@PREPROCESS_INPUT_FILES_MAIN@
+#if $additional_reads.selector == 'true'
+    @PREPROCESS_INPUT_FILES_ADDITIONAL@
+#end if
+@PREPROCESS_NANOPORE_PACBIO_FILES@
+@PREPROCESS_CONTIGS_FILES@
+@PREPROCESS_SANGER_FILES@
+
+@OMP_THREADS@
+## run
+spades.py
+    $operation_mode
+    -o 'output'    
+    @RESOURCES@
+    @INPUT_READS_MAIN@
+    #if $additional_reads.selector == 'true'
+        @INPUT_READS_ADDITIONAL@
+    #end if
+    ## additional reads
+    @NANOPORE_PACBIO@
+    @SANGER@
+    @CONTIGS@
+    ## parameter
+    #if $cov_cond.cov_cutoff == 'value':
+        --cov-cutoff $cov_cond.manual
+    #else:
+        --cov-cutoff $cov_cond.cov_cutoff
+    #end if
+    @KMER@
+    @PIPELINE_OPTIONS@
+    @PHREDOFFSET@    
+
+    ## postprocessing
+    @STATS@
+    ]]></command>
+    <inputs>
+        <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
+        <expand macro="input_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
+        <expand macro="input_additional_files_all" format="@INTYPES@" label="FASTA/FASTQ file(s)"/>
+        <section name="arf" title="Additional read files">
+            <expand macro="nanopore_pacbio"/>
+            <expand macro="sanger"/>
+            <expand macro="contigs"/>
+        </section>
+        <expand macro="pipeline_options" additional_help="&quot;Isolate&quot; is not compatible with &quot;Careful&quot; and Operation mode &quot;Only error correction&quot;">
+            <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option>
+            <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option>
+            <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option>
+            <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
+        </expand>
+        <expand macro="covcutoff"/>
+        <expand macro="kmer" help="If --sc is set the default values are 21,33,55. For multicell datasets K values are automatically selected using maximum read length."/>        
+        <expand macro="phred"/>
+        <expand macro="optional_output"/>
+    </inputs>
+    <outputs>
+        <expand macro="out_ag"/>
+        <expand macro="out_ags"/>
+        <expand macro="out_cn"/>
+        <expand macro="out_cp"/>
+        <expand macro="out_cr"/>
+        <expand macro="out_cs"/>
+        <expand macro="out_l"/>
+        <expand macro="out_sc"/>
+        <expand macro="out_sp"/>
+        <expand macro="out_ss"/>        
+    </outputs>
+    <!-- tests/help/citations unchanged -->
+</tool>
+