| Previous changeset 0:6b86c86eab26 (2023-01-12) Next changeset 2:fa35f1106d3e (2023-02-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta commit 939f7ba1b584cb940244def0b6765d2494af3b94 |
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modified:
hifiasm_meta.xml macros.xml test-data/asm.p_ctg.gfa |
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| diff -r 6b86c86eab26 -r 15dbb444df71 hifiasm_meta.xml --- a/hifiasm_meta.xml Thu Jan 12 23:07:53 2023 +0000 +++ b/hifiasm_meta.xml Wed Jan 18 09:12:38 2023 +0000 |
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| @@ -1,5 +1,5 @@ <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> + <description>for metagenome assembly using Hifi reads</description> <macros> <import>macros.xml</import> </macros> @@ -21,21 +21,24 @@ --lowq-3 '$read_selection.lowq_3' --lowq-5 '$read_selection.lowq_5' -a '$assembly.a' + #if $f: + -f '$f' + #end if -k '$overlap_correction.k' -o asm -r '$overlap_correction.r' - #if '$read_selection.S': - -S - #end if + $read_selection.S -t \${GALAXY_SLOTS:-4} '$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" /> + <!-- This hidden parameter is only used to save RAM for planemo test. --> + <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 --> + <param type="hidden" optional="true" argument="-f" /> <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='-S' type="boolean" checked="true" truevalue="-S" falsevalue="" 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." /> @@ -51,8 +54,8 @@ <outputs> <!-- contig graph files --> <collection name="contig_graphs" type="list" label="hifiasm_meta on ${on_string}: contig graphs"> + <data name="Primary contigs" label="Primary contigs" from_work_dir="asm.p_ctg.gfa" format="gfa2" /> <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"> @@ -68,8 +71,7 @@ <!-- 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" /> + <param name='f' value="0" /> <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"/> @@ -80,19 +82,21 @@ hifiasm_meta ------------ -de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. +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 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 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 binning info. -------------- @@ -101,4 +105,5 @@ This tool was wrapped by the Galaxy Australia team. ]]></help> -</tool> \ No newline at end of file + <expand macro="citations"/> +</tool> |
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| diff -r 6b86c86eab26 -r 15dbb444df71 macros.xml --- a/macros.xml Thu Jan 12 23:07:53 2023 +0000 +++ b/macros.xml Wed Jan 18 09:12:38 2023 +0000 |
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| @@ -1,11 +1,23 @@ <macros> - <token name="@TOOL_VERSION@">hamtv0.3</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">0.3</token> + <token name="@CONDA_VERSION@">hamtv0.3</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@TOOL_VERSION@">hifiasm_meta</requirement> + <requirement type="package" version="@CONDA_VERSION@">hifiasm_meta</requirement> </requirements> </xml> - <!-- no citation or bio.tools id yet! --> + <!-- no citation or bio.tools id yet --> + <xml name="citations"> + <citations> + <citation type="bibtex">@software{hifiasm-meta, + author = {xfengnefx}, + year = {2023}, + title = {hifiasm-meta}, + publisher = {GitHub}, + url = {https://github.com/xfengnefx/hifiasm-meta} + }</citation> + </citations> + </xml> </macros> |
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| diff -r 6b86c86eab26 -r 15dbb444df71 test-data/asm.p_ctg.gfa --- a/test-data/asm.p_ctg.gfa Thu Jan 12 23:07:53 2023 +0000 +++ b/test-data/asm.p_ctg.gfa Wed Jan 18 09:12:38 2023 +0000 |
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| b'@@ -2,6 +2,6 @@\n A\ts0.ctg000001l\t0\t+\tm64015_200911_223407/161286451/ccs\t0\t18043\tid:i:174\tHG:A:a\n A\ts0.ctg000001l\t17895\t+\tm64015_200911_223407/34014047/ccs\t0\t8783\tid:i:83\tHG:A:a\n A\ts0.ctg000001l\t23145\t-\tm64015_200911_223407/89456653/ccs\t0\t4988\tid:i:237\tHG:A:a\n-S\ts1.ctg000002l\tGGGGAGTAAGCTTAGTCAGCCGTTGTCTCCGGGTGTCGCGTGCGCAGTTGCACGTCATTCTCAGACGAACCGATGACTGGATGGATGGCCGCCGCAGTCGTCACACTGATGATACGGATGTGCTTCTCCGTATACACCATGTTATCGGAGAGCTGCCCACGTATGGTTATCGTCGGGTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAACCTGCTGTACCGCCATCGAAACGGGCACATACAGGCAGAGTGGCTGTGAAAGAAAGTAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCCGCTGTGATAACGGAGAAAAACTGCGAGTCACGTTCGCGCTGGACTGCTGTGACCGTGAGGCGCTGCACTGGGCGGTCACTACGGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGAGCTTCCGGCGTCTCCAGTAGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGGCAGTTTGCCCGGATGTTGGGGCTTGAACCGAAGAGCACGGCGGTGCGGAGTCCGGAGAGTAACGGCATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTGTCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCACTGGGTTATCGCTCGCCACGGGAATATCTACGGCAGCAAGCCAGTAATGGGTTAAGTGATAACAGGTGTCTGGAAATATAGGGGCAAATCCAGTTAGTGTCATTGATATATTCATTCATTGTCACAAAGTTTTTATCAGAGAAACGGTAACCAGCGAAAGTGAGCTGGCTACCGGTAGATTCAAAACGTTTTGAATAGTTAGCGCGGTAGCTATAACCCGTTTCTTTATCCTGATTATGCAACTGAGCATCAGATCGTGTGACATCAAAAGATAATGAACCTAATGAGTTAAGGTTAAAACCAACGCCGGCAGCCAGAGATTGATAATCACGGTTTGTTAAAACTGAACCACCATACAGGGATACATTGTTCAGCCAACCCCATGAGAATTCACCAGTCCAGAAGAAGGGTTGTTGTAAGGAATCACCACCAACGCTGGTCGGTTTACCCATAGCAGTGGTGTAGCGAATCTGCCCTTTACGCGTCAGATAAGGAATACTATTAGATGCAACTTGCCATTGCGTAACGCGTCCGTCCTCTTCTTCAACCTTGACGTCAAGTTGCCCCTGTAATGTATTGAATAAATTGGTAATAGCAAATGGGCCTGGAGGAACATTTTCTTGATAAATAATACGGTTGTTCTGTGAGACAGTGACCTTTGCATTCGTTTGTGCGACACCCGTGATTTGCGGTGCGTAACCACGTAGGTCTGGCGGTAACATATTCTCATCGCTTTTCAACGAAATGCCAGAAAAATGGAAAGAGTCGAAAATAGAGGATTCAGTATCGTATTGACCTATAGTTAGTTTTGCATTCATTGCTGGGATTGGGCGAAACAAATAAATACGCGGAAAATCCAGGTTGGTCGCCTGGCTTTTTGCCATTGTTAAATGACTGATCGTACTGGTAATCAGTACGCAGGCGCCAGGCCCCAAGATTAACCCCAGCCTGCCCATAGGAACTTATATTTTTGCGAATTATCGCCCTGATGTGGTGCATAATGAGAGGCATATAAATTGTAGTCAAGAAATGCCCCAGCAATACCATGATTCCAAAGTTCAGGAGGCGTCCAGTTTGCATCTTTGTATTTTAACCATGCCTGAGGTGCAGATATGGATAATTGCATTTTCCCTTTATCGAGATAAGTTGTAATTTGTTTTTCTTTTTCGATAGGGTAACAACCATCGATCAGGTTTTGCTGAGTTTTTTCAATAAATTCATCAGTAAATCCTAATAATGTTAATTGCTCTGGTGTCACGCAAACTGCAGTTTGGTTATCAATTAATACCCATTGGAGGTCAAGGTGGATTGGCGTCCTCTTATTATTAATCAGAGTGCTTAGTGAATATTTGCCGACGGGTAATTGGCCATCAGTTTCAAATTGGGAAAGGTTAACGTTTTCACGATCTTCGGCTTCGATTAAATCTTTGTTGAATTCAACGGCATAAGCTGACGCACAACCAATGATGATAACGGATAATGAACAATAAATATTTTTAATCAATTCGCTTATTGTGGTTAATTTTAATTTTTTATTACATCTGATCCACTTATCATTAATCCGTTAATGATGTGGCCGGGCGAACCCGGCCAAATGCGATTACTCGTAAGCAATCTTGTAGTCAGCCTGAGCGTAAACGTTGCCCGGGGTGGCATCTTTGCTTGGGGATTCCATACGAGCTTTGAAATTCAGTTCCTGATAGCTGTTGGTATTGTTGAACGTAATTACTACCGGAGTACCTAAAGTTACTTCGCCGCTCTGGCTGTCCAGAATACGTACGCCAACGCCAGTGGCGCCGCCGATTTCAGTTTCTTTGGTATTTTTCAGAAGATCAGACTGACCCGTCATGGTATTTGCTGTAGTGAAAGTAACCTTCGCTTTTGAATAAGTAGTTCCACCCTGACTCAGCATGCAGTCCTGCAGGTGAATAGTGAAAGGTTCAGCCAAAGATTTCTGATCGCTTTTCAGTACGGTATCTGCTACTTCACCCAGATTTACAGTTAAATCTTCGTCACCTGGTTTAATAGAACATGGAGCAGAGATAACTTCACCTTTAAATTTAACAATACCGTGACCTTCATCAGCAAACACGTTATTGGAAAGAATCATTGCTACGCCAGCAACAAGAAGTGACTTTTTAAAAGCGGACATAATATTCCTTTATATAAAGATAAGTAGAAAAGAGAATGATTAGTAACTGTTATTTAAGGACTACTAATCATTGAAATATGATATTTTATTTTGTGTTTTTTATAAAATTAGTTTATCTAAATATCGATTAAGTAAAACTTAAAAAATACATTGCAATTATACTTTCAATTGTACTCATTCATTTTTGTGATGGTTTTCTGAATGGGATTACGCGATAAGGTAATAGAAAGCACTATAAATTAGAGGATTAATTCATAATTTACAGTGCATTAAAGACGAATGTTTACAGCGTTGGGGGGAGAGTCTCTGGATCTGGCTGCTTTTTGATCTCAGTACTGCGATTTTCCAGTTCGCTGATTCTTTGTTCAAGCAGCGCCAGTTTTTCACGAGTCCGTAACAGGACTTGCGTTTGGACGTCGAACTCTTCACGGCTTACAAGGTCGAGGCGCGTCAGCTGCGCTTGTAGGGTTTGGCGGATTTTTTTCTCCACATCTTCCCCGAACTCCCTGATTCCTTTAGGCATTGATTCGTGAACCTGGCGAGCGATTTGCTCAATTTTTTTCGGGTCAATCATTGTAGTTTCCCTGTACTGATAGGTGTTGAGTGCCATTGTAGTGCGATAAGGGTAAGTCATAAACCAGAATTATGTGAAGCTATGCGTTGCTGCCGCTAATCATTAGCGTTATAGTGAATCCGCTTATTCTCAGGGCGGGGCGAAATTCCCCACCGGCGGTAAATCAACTCAGTTGAAAGCCCGCGAGCGCTTTGGGTGCGAACTCA'..b'ATAGTCCCAGTAAATGCGGACTTGGCTGGTATGCCTGGATTGACGAAGTGGTGATGATACTTGCACCTTTCGGTAGCAGGGGGATCGCTTCCTGGGTTAGCCAGAACAGCGCGAAAACGTTAATGGCAAAGGTCTTTTGAAACTGTTCGCTGGTGAGGTCTGCAATATCCGGAATGGCAACCTGTTTCCCGGCGACCAGCGCCATAATATCCAGCCCGCCTAACGCCTTGTGCGCTTCGTGAACCAGCGAACGGGCAAATTTCTCATCGCTTAAATCGCCTGGCAGCAGAACGGCTTTGCGTCCGCATTCTTCAATGATCTTTTTCACATCCTGAGCGTCTTCTTCTTCCACGGGAAGATAACTGATCGCCACGTCAGCCCCTTCACGCGCGTAAGCGATGGCGGCAGCGCGACCTATTCCGGAATCGCCCCCTGTCACCAGTGCTTTACGATCTTTCAGGCGACCGCTACCAACATAGGTTTTCTCGCCGCAATCCGGTACCGGTGTCATCTTCGCCTGGATGCCTGGCGTCGGTTGTTTCTGTTTGGGATATTCACCAGTGTAATACTGCGTGGTCGGGTCTTTTAAATGAGACATCGTTTTTCTCCCTTCAGGTTCAACGTCCTTTAAGGGTAGACGTTCTCGATGCGTTGATAAGGGAACCAGGAAGATCCCTAAACCTCAGAATTATGCGACAAAGGTTTAACGTATATGTTGATTTGCTGTTGCGTGCTGTTTACTCAATTGCGATATACTGTTGCCCGTTTTAACTACACGACAGGAATGTATGGAACGTTTTCTTGAAAATGCAATGTATGCTTCTCGCTGGCTGCTTGCCCCCGTGTACTTTGGCCTTTCGCTGGCGTTAGTTGCCCTGGCGCTGAAGTTCTTCCAGGAGATTATTCACGTACTGCCGAATATCTTCTCGATGGCGGAATCAGATTTGATCCTCGTGTTGCTGTCGCTGGTGGATATGACGCTGGTTGGCGGTTTGCTGGTGATGGTGATGTTTTCCGGTTATGAGAATTTCGTCTCACAGCTGGATATCTCCGAGAACAAAGAGAAGCTGAACTGGCTGGGGAAAATGGACGCAACGTCGCTGAAAAACAAAGTAGCAGCGTCGATTGTGGCAATTTCTTCCATTCACTTACTGCGCGTCTTTATGGATGCGAAAAATGTCCCGGATAACAAACTGATGTGGTACGTCATTATCCATCTGACGTTTGTGCTTTCTGCATTTGTGATGGGCTATCTTGACCGACTGACTCGTCATAATCACTGATCTGATTCGGGCGCGGTTCGCGCGCCCGTTATTAACAGGTCATTTATCGGAAGACGCCTGCCACAGATTCAGCTCGCCATCGGCGATATGCTGATCAATCTGCGCCAGCTCCTTGGTGCTAAATGTCAGATTATTCAGCGCCTGCACGTTCTCCTCTAGTTGCTCCGCGCGGCTGGCACCAATCAATACCGACGTCACGCGATCATCTTTCAGCAACCAGCTTAACGCCATTTGCGCCATTGATTGTCCACGCTGCTGTGCCATTTCATTCAATAAGCGCAGGCTGTTGAGGTTGGCTTCGGTAAGCATTTTCGGTGTCAGACCACGAACTTTATTCCCTTCACGATGCATCCGTGAATCTTGCGGAATGCCGTTGAGATATTTTCCGGTCAGCAATCCCTGAGCCAGAGGAGTAAAGGCAATACAGCCCACGCCGTTATTTTGCAGGGTATCCAGCAGGCCGCTTTTATCCACCCAGCGGTTCAGTAAATTGTACGAAGGTTGATGAATTAACAGCGGAATTTTCCACTCGCGCAGCAACTCGACCATTTTTTGCGTCCGCTCTGGCGAGTAAGAGGAGATCCCGACATACAGCGCCTTACCGCTTTGTACCGCATGAGCCAGCGCAGAGGCGGTTTCTTCCATCGGCGTATTTTCATCGACGCGATGAGAGTAAAAGATATCGACATACTCAAGCCCCATACGCTTCAGGCTTTGGTCGAGGCTGGCGAGCAGGTATTTACGTGAACCGCCAGAGCCCGTAAGGGCCGGGCCACATATCGTAGCCAGCCTTGGTAGAGATAATCAGTTCATCGCGATAAGCGGCAAAATCCTCCCGCAGCAGGCGACCAAAGTTCTCTTCTGCGCTTCCTGGAGGCGGCCCGTAATTGTTGGCTAAATCAAAGTGCGTAATGCCCAAATCAAACGCTTTACGCAGGATCGCACGCTGTGATTCCAGCGCGTTAACGTGACCGAAATTGTGCCATAAACCGAGCGATAACGCGGGCAGGCGTAAACCACTTTTTCCGCAATAGCGGTATTGCATCTGCCCGTAACGTTCGGGATTCGCTAACCAGACCATGACCTCTCCTTTCCACCGTTCAATTTCGAAACAATGTTTCTAGTTTAGCGATTCGCCAGCGCGTATCCCGTAGTCTGGCTCACAGAGTGACGAAAAACTGGGCAAAAATACGTGCTTATGCTTTGCTTAAAAAAACACCAACTGAGGAGTGCAACGATGCCCGCGTTTAACCGCCAAAGATTTCCCACAAGAGTTGCTGGATTACTATGACTATTACGCTCACGGGAAAATCTCGAAACGTGAGTTCCTCAACCTTGCGGCGAAGTGCGGTAGGCGGGATGACGGCATTAGCGTTGTTTGATTTGCTCAAGCCAAATTATGCGCTGGCGACTCAGGTAGAGTTTACCGACCCGGAAATTGTTGCTGAGTACATCACGTATCCTTCGCCAAATGGTCACGGCGAGGTGCGGGGTTATCTGGTGAAGCCCGCAAAGATGAGCGGCAAAACGCCAGCCGTAGTGGTGGTGCATGAGAATCGTGGACTGAATCCGTATATCGAAGATGTGGCACGGCGAGTGGCGAAGGCGGGGTATATCGCCCTGGCACCTGACGGCTTAAGTTCCGTTGGAGGTTATCCGGGAAATGATGATAAAGGTCGTGAGCTGCAACAGCAGGTTGATCCAACAAACTGATGAATGATTTCTTTGCCGCAATTGAGTTTATGCAACGCTATCCGCAAGCGACAGGCAAAGTGGGTATTACCGGATTTTGCTATGGCGGTGGCGTATCGAACGCGGCGGCTGTCGCGTATCCGGAACTGGCCTGCGCGGTGCCGTTTTATGGTCGTCAGGCACCCCACTGCCGATGTGGCGAAGATTGAAGCGCCTTTACTACTCCACTTCGCGGAACTGGACACCCGAATCAACGAGGGCTGGCCTGCTTACGAGGCGGCGTTGAAAGCCAATAATAAGGTTTATGAGGCGTATATCTATCCGGGGGTTAATCACGGATTCCATAATGATTCCACGCCCCGTTATGACAAATCTGCCGCCGATCTTGCCTGGCAAAGGACACTGAAATGGTTCGATAAATATCTCTCCTGATAGGTTTATCTCTTACGGGATTACGTCTTAAACAAGCATGAAAAAATAGCGTGCGCAAAAGTCGTTCTTTGCCTAAAATATCGCTATATATGACAATATATAGCGAATGAGGTGAACGATGAATAACCATTTTGGTAAAGGCTTAATGGCGGGATTAAAAGCAACGCATGCCGACAGTGCGGTTAATGTGACAAAATTCTGTGCCGATTATAAACGCGGTTTTGTATTAGGCTACTCACACCGGATGTACGAAAAGACCGGAGATCGCCAGCTTAGCGCCTGGGAAGCGGGTATTCTGACGCGCCGCTATGGACTGG\tLN:i:41857\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+A\ts1.ctg000002l\t18954\t+\tm64015_200911_223407/145754697/ccs\t0\t22903\tid:i:193\tHG:A:a\n' |