# HG changeset patch
# User estrain
# Date 1773404478 0
# Node ID f69397b32f52ef69d7ce490e350012d3d11fb40a
planemo upload commit 7f003a1dcc0fde7a5c85786dd154fd09836a417b
diff -r 000000000000 -r f69397b32f52 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Mar 13 12:21:18 2026 +0000
@@ -0,0 +1,634 @@
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+ 4.2.0
+ 0
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+ spades
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+ &1 | awk -F 'v' '{print $2}']]>
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+ fasta,fasta.gz
+ fastqillumina,fastqillumina.gz,fastqsanger,fastqsanger.gz
+ @FASTQ_INTYPES@,@FASTA_INTYPES@
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+ 10.1093/bioinformatics/btv688
+ 10.1093/bioinformatics/btu266
+ 10.1093/bioinformatics/btv337
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+ 1 job per pair)
+ mkdir -p paired_reads1 &&
+ #set fw_reads1 = []
+ #set rv_reads1 = []
+ #set ext = $fix_ext($singlePaired.input.forward.ext)
+ #set base = re.sub('[^\w\-_.]', '_', $singlePaired.input.element_identifier)
+ #set f1 = 'paired_reads1/' + $base + '1.' + $ext
+ #set f2 = 'paired_reads1/' + $base + '2.' + $ext
+ ln -s '$singlePaired.input.forward' '$f1' &&
+ ln -s '$singlePaired.input.reverse' '$f2' &&
+ $fw_reads1.append($f1)
+ $rv_reads1.append($f2)
+#end if
+]]>
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+ '$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.')
+#end if
+]]>
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+ [0-9,]+
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+ 'ag' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'ags' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'cn' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'cp' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'cr' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-assembler'
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+ 'cs' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'l' in optional_output
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+ 'sc' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'sp' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'ss' in optional_output
+ 'operation_mode' not in vars() or operation_mode != '--only-error-correction'
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+ 'rs' in optional_output
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+ 'b' in optional_output
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+ 'dg' in optional_output
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+ - Assembly graph
+ - Assembly graph with scaffolds
+ - Contigs
+ - Contigs paths in the assembly graph
+ - Contigs stats
+ - Corrected reads by BayesHammer
+ - Log file
+ - Scaffolds (recommended for use as resulting sequences)
+ - Scaffolds paths in the assembly graph
+ - Scaffolds stats
+ SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
+
+
+
+
diff -r 000000000000 -r f69397b32f52 spades_cpu7mem28.xml
--- /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 @@
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+ genome assembler for genomes of regular and single-cell projects
+
+ macros.xml
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+ spades
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diff -r 000000000000 -r f69397b32f52 test-data/corona_scaffold.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/corona_scaffold.fasta Fri Mar 13 12:21:18 2026 +0000
@@ -0,0 +1,18 @@
+>NODE_1_length_1009_cluster_1_candidate_1_domains_2
+GTTCAAGCTGAGGCAAAACGCCTTTTTCAACTTCTACTAAGCCACAAGTGCCATCTTTAG
+GATGTTGACGTGCCTCTGATAAGACCGCCTCCACTGGAGGATACACAGGTTTAAAGGTTT
+ATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAAC
+GAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATA
+ATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCT
+GCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGT
+GACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAAC
+TCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGG
+AGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAG
+TTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATG
+CTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTC
+AGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAG
+TGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTT
+ACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAG
+ATTTAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAA
+CAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCCTGGTCATGTTGAG
+CTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACAC
diff -r 000000000000 -r f69397b32f52 write_tsv_script.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/write_tsv_script.py Fri Mar 13 12:21:18 2026 +0000
@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+
+import re
+import sys
+
+search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)(.*\$)?"
+
+replace_str = r"\1_\2\t\3\t\4"
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+cmd = re.compile(search_str)
+
+sys.stdout.write("#name\tlength\tcoverage\n")
+
+for i, line in enumerate(sys.stdin):
+ if cmd.match(line):
+ sys.stdout.write(cmd.sub(replace_str, line))