| Next changeset 1:15dbb444df71 (2023-01-18) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 64c69504c3c9d78544ff708c1c8c819981913a7d |
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hifiasm_meta.xml macros.xml test-data/asm.a_ctg.gfa test-data/asm.p_ctg.gfa test-data/zymoD6331std-ecoli-ten-percent.42.1.fq.gz |
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| diff -r 000000000000 -r 6b86c86eab26 hifiasm_meta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hifiasm_meta.xml Thu Jan 12 23:07:53 2023 +0000 |
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| @@ -0,0 +1,104 @@ +<tool id="hifiasm_meta" name="Hifiasm_meta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>for metagenome assembly using Hifi reads.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ################## + ## SET UP FILES ## + ################## + + #set reads_fn = 'reads.' + $reads.ext + ln -s '$reads' '$reads_fn' && + + ################# + ## RUN HIFIASM ## + ################# + + hifiasm_meta + --lowq-10 '$read_selection.lowq_10' + --lowq-3 '$read_selection.lowq_3' + --lowq-5 '$read_selection.lowq_5' + -a '$assembly.a' + -k '$overlap_correction.k' + -o asm + -r '$overlap_correction.r' + #if '$read_selection.S': + -S + #end if + -t \${GALAXY_SLOTS:-4} + '$reads_fn' + + ]]></command> + <inputs> + <!-- fastq files (could be a repeat or a collection) --> + <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" /> + <section name="read_selection" title="Read selection" expanded="false"> + <param argument='-S' type="boolean" checked="true" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." /> + <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." /> + <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." /> + <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." /> + </section> + <section name="overlap_correction" title="Overlap/Error correction" expanded="false"> + <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" /> + <param argument='-r' type="integer" value='3' min="1" max="10" label="rounds of correction" /> + </section> + <section name="assembly" title="Assembly" expanded="false"> + <param argument='-a' type="integer" value='4' min="1" max="10" label="rounds of assembly cleaning" /> + </section> + </inputs> + <outputs> + <!-- contig graph files --> + <collection name="contig_graphs" type="list" label="hifiasm_meta on ${on_string}: contig graphs"> + <data name="Alternate contigs" label="Alternate contigs" from_work_dir="asm.a_ctg.gfa" format="gfa2" /> + <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" /> + </collection> + <!-- unitig graph files --> + <collection name="unitig_graphs" type="list" label="hifiasm_meta on ${on_string}: unitig graphs"> + <data name="Raw unitigs" label="Raw unitigs" from_work_dir="asm.r_utg.gfa" format="gfa2" /> + <data name="Processed unitigs" label="Processed unitigs" from_work_dir="asm.p_utg.gfa" format="gfa2" /> + </collection> + <!-- Simplified graphs for visualisation --> + <collection name="simple_graphs" type="list" label="hifiasm_meta on ${on_string}: graphs for visualisation"> + <discover_datasets pattern="(?P<designation>.+)\.noseq.gfa" format="gfa2" visible="false" /> + </collection> + </outputs> + <tests> + <!-- 01: basic function --> + <test> + <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" /> + <param name='S' value="False" /> + <param name='r' value="1" /> + <output_collection name="contig_graphs" type="list"> + <element name="Primary contigs" file="asm.p_ctg.gfa"/> + <element name="Alternate contigs" file="asm.a_ctg.gfa"/> + </output_collection> + </test> + </tests> + <help><![CDATA[ +hifiasm_meta +------------ + +de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. + + +Hifiasm is an ultrafast haplotype-resolved de novo assembler for PacBio +Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed +genome. Thus, it is able to keep the haplotype information as much as possible. +The input of hifiasm is the PacBio Hifi reads in fasta/fastq format, and its +outputs consist of multiple types of assembly graph in GFA format. + +Hifiasm_meta is a fork of hifiasm. It comes with a read selection module, which +enables the assembly of dataset of high redundancy without compromising overall +assembly quality, and meta-centric graphcleaning modules. Currently hifiasm_meta +does not take bining info. + +-------------- + +hifiasm_meta's home page is +`xfengnefx/hifiasm-meta <https://github.com/xfengnefx/hifiasm-meta>`__. + +This tool was wrapped by the Galaxy Australia team. + ]]></help> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 6b86c86eab26 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jan 12 23:07:53 2023 +0000 |
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| @@ -0,0 +1,11 @@ +<macros> + <token name="@TOOL_VERSION@">hamtv0.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">hifiasm_meta</requirement> + </requirements> + </xml> + <!-- no citation or bio.tools id yet! --> +</macros> |
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| diff -r 000000000000 -r 6b86c86eab26 test-data/asm.p_ctg.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/asm.p_ctg.gfa Thu Jan 12 23:07:53 2023 +0000 |
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@@\n+S\ts0.ctg000001l\tGCGACCTGTGATGCTCTGGTTCAGGCGCACGGCGCGTTGAAAGGGTTGGCTGCGTCACTGATGAAAATCGCCAATGATGTCCGCTGGCTGGCCTCTGGCCCCGCGCTGCGGAATTGGTGAAATCTCAATCCCGGAAAATGAGCCGGGCAGCTCAATCATGCCGGGGAAAGTGAATCCAACACAGTGTGAGGCATTAACCATGCTCTGCTGTCAGGTGATGGGGAACGACGTGGCGATCAACATGGGGGGCGCTTCCGGTAACTTTGAACTGAACGTCTTCCGTCCAATGGTGATCCACAATTTCCTGCAATCGGTGCGCTTGCTGGCAGATGGCATGGAAAGTTTTAACAAACACTGCGCAGTGGGTATTGAACCGAATCGTGAGCGAATCAATCAATTACTCAATGAATCGCTGATGCTGGTGACTGCGCTTAACACCCACATTGGTTATGACAAAGCCGCGGAGATCGCCAAAAAAGCGCATAAAGAAGGGCTGACCTTAAAAGCTGCGGCCTTGCGCTGGGGTATCTTAGCGAAGCCGAGTTTGACAGCTGGGTACGGCCAGAACAGATGGTCGGCAGTATGAAAGCCGGGCGTTAATCCGCAACATACAGGTGCAGCCGGGGAATGATCAAACGAAGCGGCTGCGCCTGTGGTTTATAACGGTGTTGCACATTGTCGGCATCGTAATTTAACAACTCCCCAACATCCGGCACGCCCGCGCCATTATCCCGATTAATCAGCGCAATAAGCGGTGTAGGGCAAGCGTGTTGTACTTGTTTTTGATCTCCTTTGTACCAGACGCGGGCAATCGGCTGCACCTTCACCGGACGTTTGATTTTTAACTTCGCGTTCTGTGGCAGGGCAGCGATATCCTGATACTCTCGCTCCAGTTTTCTTTGCCACTCCTCGCGCGTCCACGGTGCGACACTGCGTGGTGATTTCAGGCTTTTTTCCAGCTGTGCCAGGACTTCATCACGATGCAAATTTTTTAATGATATGTTTATTAGCCCAGCCAAAACGTAAAGTGGCGGGGTCGTGCAGAACGGTGAGCGTGCGGTAAGCATTAAGGGTGATCAGCCCCGGCAAATGACGATGCACCCCATTCAAAACGTGCCGCGGTGGGGAGTTCTGATTCAACCGTGACGATATGCTCGAACGTGGTCTTGAGTTTATTGATGTGCTGAATATGACTGACCAACGCTGCTTGCGAAAGGTTATCGACCTGGTAACACAACACGCCAGGCAGACGGACAGCGGCCTTGCTGCTGCGATTTTCGGACTGTTGTTGAATAAATAAATGGCGGAAATGACGCAACGCCAGCGACTGCGCGTCGTTGCCGAGATGTTGTTTTACCTCAATACGATTAAGCGGATTATGCTCATCCTCTTTTTTTACCTCCGGCAAAGAGAACACGCGGGCAACCAATAGCTTGTGTTGCTCAAGATGAGCGGCAAATGCAGCCAGCTCTTGTTCCATCTGGCGAAAAGTAGTGTTGAGTCGGTCTACGAGATCGTAACGCGCCATAATATTAACCACTTTAGTTACAACATCCTTAATTTATAGCACAGTGGTGGTGACTTGACCACCGTGCGCGTAGTGTCAAGCAGAGGGTAAATTGCGGGATGTTATGCCATAACGGCCAGCTAAACGAGAAGCGGGCACCACCCAGTTCGCTGGTGCCACAATTAACCGTACCGCCCATTGCCAGTGCTATAGAGTGGACAATTGCCAGTCCCAGCCCGCAGCCGCCGGTTGAGCGACCCCGGCTGGGATCGAGGCGAACAAAAGGTTCAAAGATATGTTCGCGGTTTTCTGGGCAATCCCTGAGCCATCATCCTCAACAATTAATGTCGCTTTATTCCCCGACAGTAGCAGGCTGGTTTCAACCGTTGAATGGCAGTAGCGCAGGGCGTTATTGAGCAAATTATCCAGCACGCGCTCCATTAAGCGCATATCCAACGCCGCATAATGGCCTTGCATGAGCGTTTTTATCCGTACCGTTTTATCGGGGCGTTACTGCCTGAATATCTGCCAGATGCGTTGACAGCCACAACGGCAGGTCTGGTTCGCTAAGATGAAGCTCGTTTTGTGGGCGATCGAGTCGGGCATAAGTCAGCAGCTCTTCAATTAAAGCTTCAAGTTGACTGATATCACGATTCAACGCCTGGGATTCGGCGGCGCTCAGGTTATCGCTCATCTCCAGTCGATAACGCAGGCGCACTAACGGTGTTCGCAGTTCGTGAGCGATACCGTCAATAAGCTGTTTTTTGCTGGCAATTAAGGCGTTGATATTGTCCGCCATCTGGTTAAATGCGACGCCAAGTCGTTCAAAGCTCGAACCCTCATCAAAGTGGATACGTTCATTGAGATGCCCATCGCCAAATCGTTGCGCCGCTGCTTCCAGTTTTAACATATCCTGCCAGTGCGGACGCATCCAGATAAACACCGGAAAGGCGAGGGAAATAGCAATAAAAGCGATCAGGGCGATATCCAGCAATCGCATTTGATGGAGGTAATAAAGATAAGGAACAGGACCAACTGCCAGCACGTAGTGGCTGCGCGGGATACGCTGCAAAAACGTGTACTGATCGTCCAGGGCGACAATTTCGCCGCCACGCAGTCGGTGCATGGAAATATCATCAAGATGGTATTTACTCAGTGGCTCGACACGCAGATCGAAAGAGAGATTTAAATCCATCTCTTTCAGCGTCTTACCCCAGTCGTGTGGGGGGATCTCACGCAATTCGCTGCGCATCAGATACAGCGAACTGTTCATCAAATCATCCAGCGACTGTTTGCCCGCGCGTTCGGCGGTAAATTTGTACACCAGCCCAACCAGCAGAGACATCACAAGGAAGCAGACAAACAATAACAGGTAAAACTGGATAAACAATTTTTTCATCGCTTATTCCCATGCATGAGGCGCAAAAAGATAGCCCTTTGTTACGCACGGTTTTAATGCGATAAGGTTCTGCGGCGTTATCGAGTAGTTTTTTTCTTAACCGCGAAATAGCCACGTCCACGCTACGATCCAGTCCGTCATAACTGACGCCGCGTAAATTTTTCAGCAATGCATCGCGGTCCATGATTTGCCCGGCATGGGTAGCTAATTCCCACAATAATTCGAAATCAGCTGTCGAGAGCGAGATTTCAGTGTTAGCCAGGGTGACTACGCGGTTGATGGGATCGATGGTCAACGTGCCGAAATGCAGGGCTTTGTAGGGAGTCAGAGACGTTTCCTGAAGACCTTTGGTCAGTGTGGCTTGCTCATTCTGACGCAAATGCAAACGTAAACGCGCTAGCAAAACAGCAGGGGGCGTCGTTTTGAGAATATAGTCGCAGGCACCCATTTCCAGTGCCAGGATGTGGTTCATATCGCTATCGAGAGAGGTTAGAAGAACAATCGGTCCAGACCACTTTGCGCGTAAATCACGACAAATGGTCATGCCGTCCTTGCCTGGTAGCATGATGTCGAGTAACACCAAATCCGGATTTTCTCGCAAAATGGTTTCTTCGGCCTGGTCGCCGCGCGGCTCTACGGTAACCTGCATATCATGTTTTGCCAGGTACGCGGCAATCAGTGAACCGACTTCCCGCATCATCTTCCACAAATACGATAGTGTTCATAACATTCACGGTAGATATAAAAACGTCACAATACACCGCGCTGTTTTTACTTACTATCAATCGTTTCTAAACAAGTTTTCATCAGGTATTCTACTGATGACTTGTTATGGAAGTGTTAAGGTAAAAAGATGGGGCTGGTAATCAAAGCCGCGCTCGGTGCGCTGGTAGTGCTGTTGATTGGTGTTTTAGCAAAAACGAAAAATTATTATATCGCCGGGCTGATTCCACTTTTCCCGACCTTTGCGCTTATCGCGCATTATATTGTTGCCAGCGAACGCGGCATTGAAGCCTTACGCGCAACCATCATTTTTAGTATGTGGTCGATTATTCCCTAT'..b'GACAATATTCACCCGAATACCTTTCTTCGCGACCTGTTTTGCCAAGCCACGGCTGTAGTTCAGAATCGCCGCCTTCGTAGCCGCATAGTCCCAGTAAATGCGGACTTGGCTGGTATGCCTGGATTGACGAAGTGGTGATGATACTTGCACCTTTCGGTAGCAGGGGGATCGCTTCCTGGGTTAGCCAGAACAGCGCGAAAACGTTAATGGCAAAGGTCTTTTGAAACTGTTCGCTGGTGAGGTCTGCAATATCCGGAATGGCAACCTGTTTCCCGGCGACCAGCGCCATAATATCCAGCCCGCCTAACGCCTTGTGCGCTTCGTGAACCAGCGAACGGGCAAATTTCTCATCGCTTAAATCGCCTGGCAGCAGAACGGCTTTGCGTCCGCATTCTTCAATGATCTTTTTCACATCCTGAGCGTCTTCTTCTTCCACGGGAAGATAACTGATCGCCACGTCAGCCCCTTCACGCGCGTAAGCGATGGCGGCAGCGCGACCTATTCCGGAATCGCCCCCTGTCACCAGTGCTTTACGATCTTTCAGGCGACCGCTACCAACATAGGTTTTCTCGCCGCAATCCGGTACCGGTGTCATCTTCGCCTGGATGCCTGGCGTCGGTTGTTTCTGTTTGGGATATTCACCAGTGTAATACTGCGTGGTCGGGTCTTTTAAATGAGACATCGTTTTTCTCCCTTCAGGTTCAACGTCCTTTAAGGGTAGACGTTCTCGATGCGTTGATAAGGGAACCAGGAAGATCCCTAAACCTCAGAATTATGCGACAAAGGTTTAACGTATATGTTGATTTGCTGTTGCGTGCTGTTTACTCAATTGCGATATACTGTTGCCCGTTTTAACTACACGACAGGAATGTATGGAACGTTTTCTTGAAAATGCAATGTATGCTTCTCGCTGGCTGCTTGCCCCCGTGTACTTTGGCCTTTCGCTGGCGTTAGTTGCCCTGGCGCTGAAGTTCTTCCAGGAGATTATTCACGTACTGCCGAATATCTTCTCGATGGCGGAATCAGATTTGATCCTCGTGTTGCTGTCGCTGGTGGATATGACGCTGGTTGGCGGTTTGCTGGTGATGGTGATGTTTTCCGGTTATGAGAATTTCGTCTCACAGCTGGATATCTCCGAGAACAAAGAGAAGCTGAACTGGCTGGGGAAAATGGACGCAACGTCGCTGAAAAACAAAGTAGCAGCGTCGATTGTGGCAATTTCTTCCATTCACTTACTGCGCGTCTTTATGGATGCGAAAAATGTCCCGGATAACAAACTGATGTGGTACGTCATTATCCATCTGACGTTTGTGCTTTCTGCATTTGTGATGGGCTATCTTGACCGACTGACTCGTCATAATCACTGATCTGATTCGGGCGCGGTTCGCGCGCCCGTTATTAACAGGTCATTTATCGGAAGACGCCTGCCACAGATTCAGCTCGCCATCGGCGATATGCTGATCAATCTGCGCCAGCTCCTTGGTGCTAAATGTCAGATTATTCAGCGCCTGCACGTTCTCCTCTAGTTGCTCCGCGCGGCTGGCACCAATCAATACCGACGTCACGCGATCATCTTTCAGCAACCAGCTTAACGCCATTTGCGCCATTGATTGTCCACGCTGCTGTGCCATTTCATTCAATAAGCGCAGGCTGTTGAGGTTGGCTTCGGTAAGCATTTTCGGTGTCAGACCACGAACTTTATTCCCTTCACGATGCATCCGTGAATCTTGCGGAATGCCGTTGAGATATTTTCCGGTCAGCAATCCCTGAGCCAGAGGAGTAAAGGCAATACAGCCCACGCCGTTATTTTGCAGGGTATCCAGCAGGCCGCTTTTATCCACCCAGCGGTTCAGTAAATTGTACGAAGGTTGATGAATTAACAGCGGAATTTTCCACTCGCGCAGCAACTCGACCATTTTTTGCGTCCGCTCTGGCGAGTAAGAGGAGATCCCGACATACAGCGCCTTACCGCTTTGTACCGCATGAGCCAGCGCAGAGGCGGTTTCTTCCATCGGCGTATTTTCATCGACGCGATGAGAGTAAAAGATATCGACATACTCAAGCCCCATACGCTTCAGGCTTTGGTCGAGGCTGGCGAGCAGGTATTTACGTGAACCGCCAGAGCCCGTAAGGGCCGGGCCACATATCGTAGCCAGCCTTGGTAGAGATAATCAGTTCATCGCGATAAGCGGCAAAATCCTCCCGCAGCAGGCGACCAAAGTTCTCTTCTGCGCTTCCTGGAGGCGGCCCGTAATTGTTGGCTAAATCAAAGTGCGTAATGCCCAAATCAAACGCTTTACGCAGGATCGCACGCTGTGATTCCAGCGCGTTAACGTGACCGAAATTGTGCCATAAACCGAGCGATAACGCGGGCAGGCGTAAACCACTTTTTCCGCAATAGCGGTATTGCATCTGCCCGTAACGTTCGGGATTCGCTAACCAGACCATGACCTCTCCTTTCCACCGTTCAATTTCGAAACAATGTTTCTAGTTTAGCGATTCGCCAGCGCGTATCCCGTAGTCTGGCTCACAGAGTGACGAAAAACTGGGCAAAAATACGTGCTTATGCTTTGCTTAAAAAAACACCAACTGAGGAGTGCAACGATGCCCGCGTTTAACCGCCAAAGATTTCCCACAAGAGTTGCTGGATTACTATGACTATTACGCTCACGGGAAAATCTCGAAACGTGAGTTCCTCAACCTTGCGGCGAAGTGCGGTAGGCGGGATGACGGCATTAGCGTTGTTTGATTTGCTCAAGCCAAATTATGCGCTGGCGACTCAGGTAGAGTTTACCGACCCGGAAATTGTTGCTGAGTACATCACGTATCCTTCGCCAAATGGTCACGGCGAGGTGCGGGGTTATCTGGTGAAGCCCGCAAAGATGAGCGGCAAAACGCCAGCCGTAGTGGTGGTGCATGAGAATCGTGGACTGAATCCGTATATCGAAGATGTGGCACGGCGAGTGGCGAAGGCGGGGTATATCGCCCTGGCACCTGACGGCTTAAGTTCCGTTGGAGGTTATCCGGGAAATGATGATAAAGGTCGTGAGCTGCAACAGCAGGTTGATCCAACAAACTGATGAATGATTTCTTTGCCGCAATTGAGTTTATGCAACGCTATCCGCAAGCGACAGGCAAAGTGGGTATTACCGGATTTTGCTATGGCGGTGGCGTATCGAACGCGGCGGCTGTCGCGTATCCGGAACTGGCCTGCGCGGTGCCGTTTTATGGTCGTCAGGCACCCCACTGCCGATGTGGCGAAGATTGAAGCGCCTTTACTACTCCACTTCGCGGAACTGGACACCCGAATCAACGAGGGCTGGCCTGCTTACGAGGCGGCGTTGAAAGCCAATAATAAGGTTTATGAGGCGTATATCTATCCGGGGGTTAATCACGGATTCCATAATGATTCCACGCCCCGTTATGACAAATCTGCCGCCGATCTTGCCTGGCAAAGGACACTGAAATGGTTCGATAAATATCTCTCCTGATAGGTTTATCTCTTACGGGATTACGTCTTAAACAAGCATGAAAAAATAGCGTGCGCAAAAGTCGTTCTTTGCCTAAAATATCGCTATATATGACAATATATAGCGAATGAGGTGAACGATGAATAACCATTTTGGTAAAGGCTTAATGGCGGGATTAAAAGCAACGCATGCCGACAGTGCGGTTAATGTGACAAAATTCTGTGCCGATTATAAACGCGGTTTTGTATTAGGCTACTCACACCGGATGTACGAAAAGACCGGAGATCGCCAGCTTAGCGCCTGGGAAGCGGGTATTCTGACGCGCCGCTATGGACTGG\tLN:i:41858\tdp:f:1\tts:B:I,1\n+A\ts1.ctg000002l\t0\t+\tm64015_200911_223407/148179444/ccs\t0\t22379\tid:i:31\tHG:A:a\n+A\ts1.ctg000002l\t18954\t+\tm64015_200911_223407/145754697/ccs\t0\t22904\tid:i:193\tHG:A:a\n' 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| diff -r 000000000000 -r 6b86c86eab26 test-data/zymoD6331std-ecoli-ten-percent.42.1.fq.gz |
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| Binary file test-data/zymoD6331std-ecoli-ten-percent.42.1.fq.gz has changed |