| Next changeset 1:cf54dafa0403 (2023-06-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko commit 82321b91d95e2edf0e91a90d9aa3d96d63603141 |
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added:
test-data/1.meryldb test-data/2.meryldb test-data/test1.fastq.gz test-data/test2.fastq.gz test-data/test3.fastq.gz test-data/test4.fastq.gz test-data/test5.fastq verkko.xml |
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| diff -r 000000000000 -r b9a78a7ca2f3 test-data/1.meryldb |
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| Binary file test-data/1.meryldb has changed |
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| diff -r 000000000000 -r b9a78a7ca2f3 test-data/2.meryldb |
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| diff -r 000000000000 -r b9a78a7ca2f3 verkko.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/verkko.xml Mon May 01 19:20:11 2023 +0000 |
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| b'@@ -0,0 +1,269 @@\n+<tool id="verkko" name="verkko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n+ <description>hybrid genome assembly pipeline</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.2</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">verkko</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #set $hififiles = []\n+ #for $i, $datafile in enumerate($hifi):\n+ #set $filename_gz = str($i) + "_hifi.fastq.gz"\n+ #set $filename = str($i) + "_hifi.fastq"\n+ #if $datafile.is_of_type("fastq") or $datafile.is_of_type("fastqsanger"):\n+ ln -s \'$datafile\' \'$filename\' &&\n+ #silent $hififiles.append($filename)\n+ #else:\n+ ln -s \'$datafile\' \'$filename_gz\' &&\n+ #silent $hififiles.append($filename_gz)\n+ #end if\n+ #end for\n+ #if $nano:\n+ #set $nanofiles = []\n+ #for $j, $ontfile in enumerate($nano):\n+ #set $filename_gz = str($j) + "_nano.fastq.gz"\n+ #set $filename = str($j) + "_nano.fastq"\n+ #if $ontfile.is_of_type("fastq") or $ontfile.is_of_type("fastqsanger"):\n+ ln -s \'${ontfile}\' \'$filename\' &&\n+ #silent $nanofiles.append($filename)\n+ #else:\n+ ln -s \'$ontfile\' \'$filename_gz\' &&\n+ #silent $nanofiles.append($filename_gz)\n+ #end if\n+ #end for\n+ #end if\n+ #if $algorithm.hap_kmer.hap_kmers == "yes":\n+ mkdir \'h1.meryl\' &&\n+ tar -xzmf \'$algorithm.hap_kmer.h1\' -C \'h1.meryl\' --strip-components 1 &&\n+ mkdir h2.meryl &&\n+ tar -xzmf \'$algorithm.hap_kmer.h2\' -C \'h2.meryl\' --strip-components 1 &&\n+ #end if\n+ verkko --hifi\n+ #for $k, $hifi_data in enumerate($hififiles):\n+ \'$hifi_data\'\n+ #end for\n+ #if $nano:\n+ --nano \n+ #for $k, $nano_data in enumerate($nanofiles):\n+ \'$nano_data\'\n+ #end for\n+ #else:\n+ --no-nano\n+ #end if\n+ $algorithm.no_correction\n+ #if $algorithm.hap_kmer.hap_kmers == "yes":\n+ --hap-kmers \'h1.meryl\' \'h2.meryl\' $algorithm.hap_kmer.type\n+ #end if\n+ #if str($algorithm.base_k):\n+ --base-k $algorithm.base_k\n+ #end if\n+ #if str($algorithm.max_k):\n+ --max-k $algorithm.max_k\n+ #end if\n+ #if str($algorithm.window):\n+ --window $algorithm.window\n+ #end if\n+ #if str($algorithm.split_bases):\n+ --split-bases $algorithm.split_bases\n+ #end if\n+ #if str($algorithm.split_reads):\n+ --split-reads $algorithm.split_reads\n+ #end if\n+ #if str($algorithm.min_ont_length):\n+ --min-ont-length $algorithm.min_ont_length\n+ #end if\n+ #if str($algorithm.correct_k_mer_size):\n+ --correct-k-mer-size $algorithm.correct_k_mer_size\n+ #end if\n+ #if str($algorithm.correct_mer_threshold):\n+ --correct-mer-threshold $algorithm.correct_mer_threshold\n+ #end if\n+ #if str($algorithm.correct_min_read_length):\n+ --correct-min-read-length $algorithm.correct_min_read_length\n+ #end if\n+ #if str($algorithm.correct_min_overlap_length):\n+ --correct-min-overlap-length $algorithm.correct_min_overlap_length\n+ #end if\n+ #if str($algorithm.correct_hash_bits):\n+ --correct-hash-bits $algorithm.correct_hash_bits\n+ #end if\n+ #if str($algorithm.seed_min_length):\n+ --seed-min-length $algorithm.seed_min_length\n+ #end if\n+ #if str($algorithm.seed_max_length):\n+ --seed-max-length $algor'..b' value="29"/>\n+ <param name="seed_max_length" value="9999"/>\n+ <param name="align_bandwidth" value="14"/>\n+ <param name="score_fraction" value=".98"/>\n+ <param name="min_identity" value=".84"/>\n+ <param name="min_score" value="5001"/>\n+ <param name="end_clipping" value="99"/>\n+ <param name="incompatible_cutoff" value=".14"/>\n+ </section>\n+ <assert_command>\n+ <has_text_matching expression="verkko --hifi"/>\n+ <has_text_matching expression="--nano"/>\n+ <has_text_matching expression="--base-k 1003"/>\n+ <has_text_matching expression="--max-k 15001"/>\n+ <has_text_matching expression="--window 99"/>\n+ <has_text_matching expression="--split-bases 3000000001"/>\n+ <has_text_matching expression="--split-reads 150001"/>\n+ <has_text_matching expression="--min-ont-length 2"/>\n+ <has_text_matching expression="--correct-k-mer-size 29"/>\n+ <has_text_matching expression="--correct-mer-threshold 19"/>\n+ <has_text_matching expression="--correct-min-read-length 4001"/>\n+ <has_text_matching expression="--correct-min-overlap-length 2001"/>\n+ <has_text_matching expression="--correct-hash-bits 24"/>\n+ <has_text_matching expression="--seed-min-length 29"/>\n+ <has_text_matching expression="--seed-max-length 9999"/>\n+ <has_text_matching expression="--align-bandwidth 14 "/>\n+ <has_text_matching expression="--score-fraction 0.98"/>\n+ <has_text_matching expression="--min-identity 0.84"/>\n+ <has_text_matching expression="--min-score 5001"/>\n+ <has_text_matching expression="--end-clipping 99"/>\n+ <has_text_matching expression=" --incompatible-cutoff 0.14"/>\n+ </assert_command>\n+ <assert_stderr>\n+ <has_text text="job count min threads max threads"/>\n+ </assert_stderr>\n+ </test>\n+ <test expect_exit_code="1" expect_failure="true">\n+ <!-- No nano, use haplo, no canu correction -->\n+ <param name="hifi" value="test5.fastq,test1.fastq.gz"/>\n+ <section name="algorithm">\n+ <conditional name="hap_kmer">\n+ <param name="hap_kmers" value="yes"/>\n+ <param name="h1" value="1.meryldb"/>\n+ <param name="h2" value="2.meryldb"/>\n+ <param name="type" value="trio"/>\n+ </conditional>\n+ <param name="no-correction" value=""/>\n+ </section>\n+ <assert_command>\n+ <has_text_matching expression="verkko --hifi"/>\n+ <has_text_matching expression="--no-nano"/>\n+ <has_text_matching expression="--hap-kmers \'h1.meryl\' \'h2.meryl\' trio"/>\n+ </assert_command>\n+ <assert_stderr>\n+ <has_text text="job count min threads max threads"/>\n+ </assert_stderr>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. Verkko is Finnish for net, mesh and graph.\n+\n+ Verkko uses Canu to correct remaining errors in the HiFi reads, builds a multiplex de Bruijn graph using MBG, aligns the Oxford Nanopore reads to the graph using GraphAligner, progressively resolves loops and tangles first with the HiFi reads then with the aligned Oxford Nanopore reads, and finally creates contig consensus sequences using Canu\'s consensus module. \n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1101/2022.06.24.497523</citation>\n+ </citations>\n+</tool>\n' |