| Previous changeset 1:15dbb444df71 (2023-01-18) Next changeset 3:213df31ba341 (2024-02-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta commit bc8759245f44924d0122276e42f02fc1f1190e50 |
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modified:
hifiasm_meta.xml macros.xml |
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added:
test-data/S.a_ctg.gfa test-data/S.p_ctg.gfa test-data/tiny.fa.gz |
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| diff -r 15dbb444df71 -r fa35f1106d3e hifiasm_meta.xml --- a/hifiasm_meta.xml Wed Jan 18 09:12:38 2023 +0000 +++ b/hifiasm_meta.xml Mon Feb 06 12:20:38 2023 +0000 |
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| @@ -17,17 +17,26 @@ ################# hifiasm_meta - --lowq-10 '$read_selection.lowq_10' - --lowq-3 '$read_selection.lowq_3' - --lowq-5 '$read_selection.lowq_5' - -a '$assembly.a' + + ## bloom filter parameter #if $f: -f '$f' #end if + + ## read selection parameters + #if $read_selection.forced_read_selection.force_rs == "yes": + --force-rs + --lowq-10 '$read_selection.forced_read_selection.lowq_10' + --lowq-3 '$read_selection.forced_read_selection.lowq_3' + --lowq-5 '$read_selection.forced_read_selection.lowq_5' + #else + $read_selection.forced_read_selection.S + #end if + + -a '$assembly.a' -k '$overlap_correction.k' -o asm -r '$overlap_correction.r' - $read_selection.S -t \${GALAXY_SLOTS:-4} '$reads_fn' @@ -38,10 +47,20 @@ <!-- 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" 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." /> + <conditional name="forced_read_selection"> + <param argument="--force-rs" type="select" label="Force read selection" help="Drop reads according to configurable runtime kmer frequency thresholds"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <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" /> + </when> + <when value="no"> + <param argument='-S' type="boolean" checked="false" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps. If the estimation seems acceptable, no read will be dropped; otherwise, reads will be dropped from the most redundant ones until the criteria are satisfied. This can only be enabled if forced read selection is disabled." /> + </when> + </conditional> </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" /> @@ -77,6 +96,30 @@ <element name="Alternate contigs" file="asm.a_ctg.gfa"/> </output_collection> </test> + <!-- 02: forced read selection --> + <test> + <param name="reads" value="tiny.fa.gz" /> + <param name='f' value="0" /> + <param name='force_rs' value='yes' /> + <output_collection name="contig_graphs" type="list"> + <element name="Primary contigs"> + <assert_contents> + <has_size value="93053" delta="30000" /> + </assert_contents> + </element> + </output_collection> + </test> + <!-- 03: read selection --> + <test> + <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" /> + <param name='f' value="0" /> + <param name='force_rs' value='no' /> + <param name='S' value='true' /> + <output_collection name="contig_graphs" type="list"> + <element name="Primary contigs" file="S.p_ctg.gfa"/> + <element name="Alternate contigs" file="S.a_ctg.gfa"/> + </output_collection> + </test> </tests> <help><![CDATA[ hifiasm_meta |
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| diff -r 15dbb444df71 -r fa35f1106d3e macros.xml --- a/macros.xml Wed Jan 18 09:12:38 2023 +0000 +++ b/macros.xml Mon Feb 06 12:20:38 2023 +0000 |
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| @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">0.3</token> - <token name="@CONDA_VERSION@">hamtv0.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">0.3.1</token> + <token name="@CONDA_VERSION@">hamtv0.3.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements> |
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| diff -r 15dbb444df71 -r fa35f1106d3e test-data/S.p_ctg.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/S.p_ctg.gfa Mon Feb 06 12:20:38 2023 +0000 |
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| b'@@ -0,0 +1,7 @@\n+S\ts0.ctg000001l\tGCGACCTGTGATGCTCTGGTTCAGGCGCACGGCGCGTTGAAAGGGTTGGCTGCGTCACTGATGAAAATCGCCAATGATGTCCGCTGGCTGGCCTCTGGCCCCGCGCTGCGGAATTGGTGAAATCTCAATCCCGGAAAATGAGCCGGGCAGCTCAATCATGCCGGGGAAAGTGAATCCAACACAGTGTGAGGCATTAACCATGCTCTGCTGTCAGGTGATGGGGAACGACGTGGCGATCAACATGGGGGGCGCTTCCGGTAACTTTGAACTGAACGTCTTCCGTCCAATGGTGATCCACAATTTCCTGCAATCGGTGCGCTTGCTGGCAGATGGCATGGAAAGTTTTAACAAACACTGCGCAGTGGGTATTGAACCGAATCGTGAGCGAATCAATCAATTACTCAATGAATCGCTGATGCTGGTGACTGCGCTTAACACCCACATTGGTTATGACAAAGCCGCGGAGATCGCCAAAAAAGCGCATAAAGAAGGGCTGACCTTAAAAGCTGCGGCCTTGCGCTGGGGTATCTTAGCGAAGCCGAGTTTGACAGCTGGGTACGGCCAGAACAGATGGTCGGCAGTATGAAAGCCGGGCGTTAATCCGCAACATACAGGTGCAGCCGGGGAATGATCAAACGAAGCGGCTGCGCCTGTGGTTTATAACGGTGTTGCACATTGTCGGCATCGTAATTTAACAACTCCCCAACATCCGGCACGCCCGCGCCATTATCCCGATTAATCAGCGCAATAAGCGGTGTAGGGCAAGCGTGTTGTACTTGTTTTTGATCTCCTTTGTACCAGACGCGGGCAATCGGCTGCACCTTCACCGGACGTTTGATTTTTAACTTCGCGTTCTGTGGCAGGGCAGCGATATCCTGATACTCTCGCTCCAGTTTTCTTTGCCACTCCTCGCGCGTCCACGGTGCGACACTGCGTGGTGATTTCAGGCTTTTTTCCAGCTGTGCCAGGACTTCATCACGATGCAAATTTTTTAATGATATGTTTATTAGCCCAGCCAAAACGTAAAGTGGCGGGGTCGTGCAGAACGGTGAGCGTGCGGTAAGCATTAAGGGTGATCAGCCCCGGCAAATGACGATGCACCCCATTCAAAACGTGCCGCGGTGGGGAGTTCTGATTCAACCGTGACGATATGCTCGAACGTGGTCTTGAGTTTATTGATGTGCTGAATATGACTGACCAACGCTGCTTGCGAAAGGTTATCGACCTGGTAACACAACACGCCAGGCAGACGGACAGCGGCCTTGCTGCTGCGATTTTCGGACTGTTGTTGAATAAATAAATGGCGGAAATGACGCAACGCCAGCGACTGCGCGTCGTTGCCGAGATGTTGTTTTACCTCAATACGATTAAGCGGATTATGCTCATCCTCTTTTTTTACCTCCGGCAAAGAGAACACGCGGGCAACCAATAGCTTGTGTTGCTCAAGATGAGCGGCAAATGCAGCCAGCTCTTGTTCCATCTGGCGAAAAGTAGTGTTGAGTCGGTCTACGAGATCGTAACGCGCCATAATATTAACCACTTTAGTTACAACATCCTTAATTTATAGCACAGTGGTGGTGACTTGACCACCGTGCGCGTAGTGTCAAGCAGAGGGTAAATTGCGGGATGTTATGCCATAACGGCCAGCTAAACGAGAAGCGGGCACCACCCAGTTCGCTGGTGCCACAATTAACCGTACCGCCCATTGCCAGTGCTATAGAGTGGACAATTGCCAGTCCCAGCCCGCAGCCGCCGGTTGAGCGACCCCGGCTGGGATCGAGGCGAACAAAAGGTTCAAAGATATGTTCGCGGTTTTCTGGGCAATCCCTGAGCCATCATCCTCAACAATTAATGTCGCTTTATTCCCCGACAGTAGCAGGCTGGTTTCAACCGTTGAATGGCAGTAGCGCAGGGCGTTATTGAGCAAATTATCCAGCACGCGCTCCATTAAGCGCATATCCAACGCCGCATAATGGCCTTGCATGAGCGTTTTTATCCGTACCGTTTTATCGGGGCGTTACTGCCTGAATATCTGCCAGATGCGTTGACAGCCACAACGGCAGGTCTGGTTCGCTAAGATGAAGCTCGTTTTGTGGGCGATCGAGTCGGGCATAAGTCAGCAGCTCTTCAATTAAAGCTTCAAGTTGACTGATATCACGATTCAACGCCTGGGATTCGGCGGCGCTCAGGTTATCGCTCATCTCCAGTCGATAACGCAGGCGCACTAACGGTGTTCGCAGTTCGTGAGCGATACCGTCAATAAGCTGTTTTTTGCTGGCAATTAAGGCGTTGATATTGTCCGCCATCTGGTTAAATGCGACGCCAAGTCGTTCAAAGCTCGAACCCTCATCAAAGTGGATACGTTCATTGAGATGCCCATCGCCAAATCGTTGCGCCGCTGCTTCCAGTTTTAACATATCCTGCCAGTGCGGACGCATCCAGATAAACACCGGAAAGGCGAGGGAAATAGCAATAAAAGCGATCAGGGCGATATCCAGCAATCGCATTTGATGGAGGTAATAAAGATAAGGAACAGGACCAACTGCCAGCACGTAGTGGCTGCGCGGGATACGCTGCAAAAACGTGTACTGATCGTCCAGGGCGACAATTTCGCCGCCACGCAGTCGGTGCATGGAAATATCATCAAGATGGTATTTACTCAGTGGCTCGACACGCAGATCGAAAGAGAGATTTAAATCCATCTCTTTCAGCGTCTTACCCCAGTCGTGTGGGGGGATCTCACGCAATTCGCTGCGCATCAGATACAGCGAACTGTTCATCAAATCATCCAGCGACTGTTTGCCCGCGCGTTCGGCGGTAAATTTGTACACCAGCCCAACCAGCAGAGACATCACAAGGAAGCAGACAAACAATAACAGGTAAAACTGGATAAACAATTTTTTCATCGCTTATTCCCATGCATGAGGCGCAAAAAGATAGCCCTTTGTTACGCACGGTTTTAATGCGATAAGGTTCTGCGGCGTTATCGAGTAGTTTTTTTCTTAACCGCGAAATAGCCACGTCCACGCTACGATCCAGTCCGTCATAACTGACGCCGCGTAAATTTTTCAGCAATGCATCGCGGTCCATGATTTGCCCGGCATGGGTAGCTAATTCCCACAATAATTCGAAATCAGCTGTCGAGAGCGAGATTTCAGTGTTAGCCAGGGTGACTACGCGGTTGATGGGATCGATGGTCAACGTGCCGAAATGCAGGGCTTTGTAGGGAGTCAGAGACGTTTCCTGAAGACCTTTGGTCAGTGTGGCTTGCTCATTCTGACGCAAATGCAAACGTAAACGCGCTAGCAAAACAGCAGGGGGCGTCGTTTTGAGAATATAGTCGCAGGCACCCATTTCCAGTGCCAGGATGTGGTTCATATCGCTATCGAGAGAGGTTAGAAGAACAATCGGTCCAGACCACTTTGCGCGTAAATCACGACAAATGGTCATGCCGTCCTTGCCTGGTAGCATGATGTCGAGTAACACCAAATCCGGATTTTCTCGCAAAATGGTTTCTTCGGCCTGGTCGCCGCGCGGCTCTACGGTAACCTGCATATCATGTTTTGCCAGGTACGCGGCAATCAGTGAACCGACTTCCCGCATCATCTTCCACAAATACGATAGTGTTCATAACATTCACGGTAGATATAAAAACGTCACAATACACCGCGCTGTTTTTACTTACTATCAATCGTTTCTAAACAAGTTTTCATCAGGTATTCTACTGATGACTTGTTATGGAAGTGTTAAGGTAAAAAGATGGGGCTGGTAATCAAAGCCGCGCTCGGTGCGCTGGTAGTGCTGTTGATTGGTGTTTTAGCAAAAACGAAAAATTATTATATCGCCGGGCTGATTCCACTTTTCCCGACCTTTGCGCTTATCGCGCATTATATTGTTGCCAGCGAACGCGGCATTGAAGCCTTACGCGCAACCATCATTTTTAGTATGTGGTCGATTATTCCCTAT'..b'GACAATATTCACCCGAATACCTTTCTTCGCGACCTGTTTTGCCAAGCCACGGCTGTAGTTCAGAATCGCCGCCTTCGTAGCCGCATAGTCCCAGTAAATGCGGACTTGGCTGGTATGCCTGGATTGACGAAGTGGTGATGATACTTGCACCTTTCGGTAGCAGGGGGATCGCTTCCTGGGTTAGCCAGAACAGCGCGAAAACGTTAATGGCAAAGGTCTTTTGAAACTGTTCGCTGGTGAGGTCTGCAATATCCGGAATGGCAACCTGTTTCCCGGCGACCAGCGCCATAATATCCAGCCCGCCTAACGCCTTGTGCGCTTCGTGAACCAGCGAACGGGCAAATTTCTCATCGCTTAAATCGCCTGGCAGCAGAACGGCTTTGCGTCCGCATTCTTCAATGATCTTTTTCACATCCTGAGCGTCTTCTTCTTCCACGGGAAGATAACTGATCGCCACGTCAGCCCCTTCACGCGCGTAAGCGATGGCGGCAGCGCGACCTATTCCGGAATCGCCCCCTGTCACCAGTGCTTTACGATCTTTCAGGCGACCGCTACCAACATAGGTTTTCTCGCCGCAATCCGGTACCGGTGTCATCTTCGCCTGGATGCCTGGCGTCGGTTGTTTCTGTTTGGGATATTCACCAGTGTAATACTGCGTGGTCGGGTCTTTTAAATGAGACATCGTTTTTCTCCCTTCAGGTTCAACGTCCTTTAAGGGTAGACGTTCTCGATGCGTTGATAAGGGAACCAGGAAGATCCCTAAACCTCAGAATTATGCGACAAAGGTTTAACGTATATGTTGATTTGCTGTTGCGTGCTGTTTACTCAATTGCGATATACTGTTGCCCGTTTTAACTACACGACAGGAATGTATGGAACGTTTTCTTGAAAATGCAATGTATGCTTCTCGCTGGCTGCTTGCCCCCGTGTACTTTGGCCTTTCGCTGGCGTTAGTTGCCCTGGCGCTGAAGTTCTTCCAGGAGATTATTCACGTACTGCCGAATATCTTCTCGATGGCGGAATCAGATTTGATCCTCGTGTTGCTGTCGCTGGTGGATATGACGCTGGTTGGCGGTTTGCTGGTGATGGTGATGTTTTCCGGTTATGAGAATTTCGTCTCACAGCTGGATATCTCCGAGAACAAAGAGAAGCTGAACTGGCTGGGGAAAATGGACGCAACGTCGCTGAAAAACAAAGTAGCAGCGTCGATTGTGGCAATTTCTTCCATTCACTTACTGCGCGTCTTTATGGATGCGAAAAATGTCCCGGATAACAAACTGATGTGGTACGTCATTATCCATCTGACGTTTGTGCTTTCTGCATTTGTGATGGGCTATCTTGACCGACTGACTCGTCATAATCACTGATCTGATTCGGGCGCGGTTCGCGCGCCCGTTATTAACAGGTCATTTATCGGAAGACGCCTGCCACAGATTCAGCTCGCCATCGGCGATATGCTGATCAATCTGCGCCAGCTCCTTGGTGCTAAATGTCAGATTATTCAGCGCCTGCACGTTCTCCTCTAGTTGCTCCGCGCGGCTGGCACCAATCAATACCGACGTCACGCGATCATCTTTCAGCAACCAGCTTAACGCCATTTGCGCCATTGATTGTCCACGCTGCTGTGCCATTTCATTCAATAAGCGCAGGCTGTTGAGGTTGGCTTCGGTAAGCATTTTCGGTGTCAGACCACGAACTTTATTCCCTTCACGATGCATCCGTGAATCTTGCGGAATGCCGTTGAGATATTTTCCGGTCAGCAATCCCTGAGCCAGAGGAGTAAAGGCAATACAGCCCACGCCGTTATTTTGCAGGGTATCCAGCAGGCCGCTTTTATCCACCCAGCGGTTCAGTAAATTGTACGAAGGTTGATGAATTAACAGCGGAATTTTCCACTCGCGCAGCAACTCGACCATTTTTTGCGTCCGCTCTGGCGAGTAAGAGGAGATCCCGACATACAGCGCCTTACCGCTTTGTACCGCATGAGCCAGCGCAGAGGCGGTTTCTTCCATCGGCGTATTTTCATCGACGCGATGAGAGTAAAAGATATCGACATACTCAAGCCCCATACGCTTCAGGCTTTGGTCGAGGCTGGCGAGCAGGTATTTACGTGAACCGCCAGAGCCCGTAAGGGCCGGGCCACATATCGTAGCCAGCCTTGGTAGAGATAATCAGTTCATCGCGATAAGCGGCAAAATCCTCCCGCAGCAGGCGACCAAAGTTCTCTTCTGCGCTTCCTGGAGGCGGCCCGTAATTGTTGGCTAAATCAAAGTGCGTAATGCCCAAATCAAACGCTTTACGCAGGATCGCACGCTGTGATTCCAGCGCGTTAACGTGACCGAAATTGTGCCATAAACCGAGCGATAACGCGGGCAGGCGTAAACCACTTTTTCCGCAATAGCGGTATTGCATCTGCCCGTAACGTTCGGGATTCGCTAACCAGACCATGACCTCTCCTTTCCACCGTTCAATTTCGAAACAATGTTTCTAGTTTAGCGATTCGCCAGCGCGTATCCCGTAGTCTGGCTCACAGAGTGACGAAAAACTGGGCAAAAATACGTGCTTATGCTTTGCTTAAAAAAACACCAACTGAGGAGTGCAACGATGCCCGCGTTTAACCGCCAAAGATTTCCCACAAGAGTTGCTGGATTACTATGACTATTACGCTCACGGGAAAATCTCGAAACGTGAGTTCCTCAACCTTGCGGCGAAGTGCGGTAGGCGGGATGACGGCATTAGCGTTGTTTGATTTGCTCAAGCCAAATTATGCGCTGGCGACTCAGGTAGAGTTTACCGACCCGGAAATTGTTGCTGAGTACATCACGTATCCTTCGCCAAATGGTCACGGCGAGGTGCGGGGTTATCTGGTGAAGCCCGCAAAGATGAGCGGCAAAACGCCAGCCGTAGTGGTGGTGCATGAGAATCGTGGACTGAATCCGTATATCGAAGATGTGGCACGGCGAGTGGCGAAGGCGGGGTATATCGCCCTGGCACCTGACGGCTTAAGTTCCGTTGGAGGTTATCCGGGAAATGATGATAAAGGTCGTGAGCTGCAACAGCAGGTTGATCCAACAAACTGATGAATGATTTCTTTGCCGCAATTGAGTTTATGCAACGCTATCCGCAAGCGACAGGCAAAGTGGGTATTACCGGATTTTGCTATGGCGGTGGCGTATCGAACGCGGCGGCTGTCGCGTATCCGGAACTGGCCTGCGCGGTGCCGTTTTATGGTCGTCAGGCACCCCACTGCCGATGTGGCGAAGATTGAAGCGCCTTTACTACTCCACTTCGCGGAACTGGACACCCGAATCAACGAGGGCTGGCCTGCTTACGAGGCGGCGTTGAAAGCCAATAATAAGGTTTATGAGGCGTATATCTATCCGGGGGTTAATCACGGATTCCATAATGATTCCACGCCCCGTTATGACAAATCTGCCGCCGATCTTGCCTGGCAAAGGACACTGAAATGGTTCGATAAATATCTCTCCTGATAGGTTTATCTCTTACGGGATTACGTCTTAAACAAGCATGAAAAAATAGCGTGCGCAAAAGTCGTTCTTTGCCTAAAATATCGCTATATATGACAATATATAGCGAATGAGGTGAACGATGAATAACCATTTTGGTAAAGGCTTAATGGCGGGATTAAAAGCAACGCATGCCGACAGTGCGGTTAATGTGACAAAATTCTGTGCCGATTATAAACGCGGTTTTGTATTAGGCTACTCACACCGGATGTACGAAAAGACCGGAGATCGCCAGCTTAGCGCCTGGGAAGCGGGTATTCTGACGCGCCGCTATGGACTGG\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\t22903\tid:i:193\tHG:A:a\n' 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| diff -r 15dbb444df71 -r fa35f1106d3e test-data/tiny.fa.gz |
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| Binary file test-data/tiny.fa.gz has changed |