| Previous changeset 6:3f4d6399997b (2019-05-06) Next changeset 8:53c0b7a1a0c3 (2020-04-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b1883bac95e73fc6ffe2a36db3115ad5e5a1eba4" |
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modified:
minimap2.xml |
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added:
test-data/minimap2-self-homology.bam test-data/minimap2-self-homology.fasta |
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| diff -r 3f4d6399997b -r b3eab4b67562 minimap2.xml --- a/minimap2.xml Mon May 06 09:34:30 2019 -0400 +++ b/minimap2.xml Fri Oct 11 13:27:18 2019 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@" profile="17.01"> +<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy0" profile="17.01"> <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> <macros> <token name="@TOOL_VERSION@">2.17</token> @@ -17,7 +17,11 @@ ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if minimap2 - -x $analysis_type_selector + #if str($analysis_type_selector) == 'self-homology': + -DP -k19 -w19 -m200 + #else + -x $analysis_type_selector + #end if ## indexing options $indexing_options.H #if $indexing_options.k: @@ -113,11 +117,13 @@ -a | samtools sort -@\${GALAXY_SLOTS:-2} + -T "\${TMPDIR:-.}" -O $io_options.output_format -o '$alignment_output' #else if $io_options.output_format == 'CRAM': -a | samtools sort + -T "\${TMPDIR:-.}" -@\${GALAXY_SLOTS:-2} -O $io_options.output_format $io_options.eqx @@ -186,6 +192,7 @@ <option value="asm20">Long assembly to reference mapping (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100). Up to 20% sequence divergence.</option> <option value="splice">Long-read spliced alignment (-k15 -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --splice-flank=yes). In the splice mode, 1) long deletions are taken as introns and represented as the `N' CIGAR operator 2) long insertions are disabled 3) deletion and insertion gap costs are different during chaining 4) the computation of the `ms' tag ignores introns to demote hits to pseudogenes.</option> <option value="sr">Short single-end reads without splicing (-k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no)</option> + <option value="self-homology">Construct a self-homology map - use same genome as query and reference (-DP -k19 -w19 -m200)</option> </param> <section name="mapping_options" title="Set advanced mapping options" help="Sets -f, -g, -G, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False"> <param argument="-f" type="float" value="" optional="true" label="filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/> @@ -331,6 +338,15 @@ <param name="output_format" value="paf"/> <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> </test> + <test> + <!-- test self-homology mode --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" /> + <param name="analysis_type_selector" value="self-homology" /> + <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" /> + </test> </tests> <help> @@ -448,6 +464,13 @@ For cross-species full-genome alignment, the scoring system needs to be tuned according to the sequence divergence. +Self-homology map creation +^^^^^^^^^^^^^^^^^^^^^^^^^^ + +A self-homology map is created by mapping a genome (e.g. that of E. coli) +against itself. When this option is used the same FASTA file should +be used for reference and for the (single ended mode) query. + Advanced features ~~~~~~~~~~~~~~~~~ |
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| diff -r 3f4d6399997b -r b3eab4b67562 test-data/minimap2-self-homology.bam |
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| Binary file test-data/minimap2-self-homology.bam has changed |
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| diff -r 3f4d6399997b -r b3eab4b67562 test-data/minimap2-self-homology.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minimap2-self-homology.fasta Fri Oct 11 13:27:18 2019 -0400 |
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| b'@@ -0,0 +1,501 @@\n+>Chromosome dna:chromosome chromosome:ASM19595v2:Chromosome:1:4411532:1 REF\n+ACCAGGCAGTGACCAACGTCGATCGCACCGTGCGCTCGGTCAAGCGACACATGGGCAGCG\n+ACTGGTCCATAGAGATTGACGGCAAGAAATACACCGCGCCGGAGATCAGCGCCCGCATTC\n+TGATGAAGCTGAAGCGCGACGCCGAGGCCTACCTCGGTGAGGACATTACCGACGCGGTTA\n+TCACGACGCCCGCCTACTTCAATGACGCCCAGCGTCAGGCCACCAAGGACGCCGGCCAGA\n+TCGCCGGCCTCAACGTGCTGCGGATCGTCAACGAGCCGACCGCGGCCGCGCTGGCCTACG\n+GCCTCGACAAGGGCGAGAAGGAGCAGCGAATCCTGGTCTTCGACTTGGGTGGTGGCACTT\n+TCGACGTTTCCCTGCTGGAGATCGGCGAGGGTGTGGTTGAGGTCCGTGCCACTTCGGGTG\n+ACAACCACCTCGGCGGCGACGACTGGGACCAGCGGGTCGTCGATTGGCTGGTGGACAAGT\n+TCAAGGGCACCAGCGGCATCGATCTGACCAAGGACAAGATGGCGATGCAGCGGCTGCGGG\n+AAGCCGCCGAGAAGGCAAAGATCGAGCTGAGTTCGAGTCAGTCCACCTCGATCAACCTGC\n+CCTACATCACCGTCGACGCCGACAAGAACCCGTTGTTCTTAGACGAGCAGCTGACCCGCG\n+CGGAGTTCCAACGGATCACTCAGGACCTGCTGGACCGCACTCGCAAGCCGTTCCAGTCGG\n+TGATCGCTGACACCGGCATTTCGGTGTCGGAGATCGATCACGTTGTGCTCGTGGGTGGTT\n+CGACCCGGATGCCCGCGGTGACCGATCTGGTCAAGGAACTCACCGGCGGCAAGGAACCCA\n+ACAAGGGCGTCAACCCCGATGAGGTTGTCGCGGTGGGAGCCGCTCTGCAGGCCGGCGTCC\n+TCAAGGGCGAGGTGAAAGACGTTCTGCTGCTTGATGTTACCCCGCTGAGCCTGGGTATCG\n+AGACCAAGGGCGGGGTGATGACCAGGCTCATCGAGCGCAACACCACGATCCCCACCAAGC\n+GGTCGGAGACTTTCACCACCGCCGACGACAACCAACCGTCGGTGCAGATCCAGGTCTATC\n+AGGGGGAGCGTGAGATCGCCGCGCACAACAAGTTGCTCGGGTCCTTCGAGCTGACCGGCA\n+TCCCGCCGGCGCCGCGGGGGATTCCGCAGATCGAGGTCACTTTCGACATCGACGCCAACG\n+GCATTGTGCACGTCACCGCCAAGGACAAGGGCACCGGCAAGGAGAACACGATCCGAATCC\n+AGGAAGGCTCGGGCCTGTCCAAGGAAGACATTGACCGCATGATCAAGGACGCCGAAGCGC\n+ACGCCGAGGAGGATCGCAAGCGTCGCGAGGAGGCCGATGTTCGTAATCAAGCCGAGACAT\n+TGGTCTACCAGACGGAGAAGTTCGTCAAAGAACAGCGTGAGGCCGAGGGTGGTTCGAAGG\n+TACCTGAAGACACGCTGAACAAGGTTGATGCCGCGGTGGCGGAAGCGAAGGCGGCACTTG\n+GCGGATCGGATATTTCGGCCATCAAGTCGGCGATGGAGAAGCTGGGCCAGGAGTCGCAGG\n+CTCTGGGGCAAGCGATCTACGAAGCAGCTCAGGCTGCGTCACAGGCCACTGGCGCTGCCC\n+ACCCCGGCGGCGAGCCGGGCGGTGCCCACCCCGGCTCGGCTGATGACGTTGTGGACGCGG\n+AGGTGGTCGACGACGGCCGGGAGGCCAAGTGACGGACGGAAATCAAAAGCCGGATGGCAA\n+TTCGGGCGAACAGGTAACCGTCACTGACAAGCGGCGGATCGATCCCGAGACGGGTGAAGT\n+GCGGCACGTCCCTCCCGGCGACATGCCGGGAGGGACGGCTGCGGCCGATGCGGCGCACAC\n+CGAAGACAAGGTCGCCGAGCTGACCGCCGATCTGCAACGCGTGCAGGCCGACTTCGCCAA\n+CTACCGTAAGCGGGCGTTGCGCGATCAGCAGGCGGCCGCTGACCGAGCCAAGGCCAGCGT\n+TGTCAGCCAATTGCTGGGTGTACTGGACGATCTCGAGCGGGCGCGCAAGCACGGCGATTT\n+GGAGTCGGGTCCACTGAAGTCGGTCGCCGACAAGCTAGACAGCGCGTTGACCGGGCTGGG\n+TCTGGTGGCGTTCGGTGCCGAGGGCGAGGATTTCGACCCCGTGCTGCACGAAGCGGTGCA\n+ACACGAGGGCGACGGCGGGCAGGGGTCCAAGCCGGTAATCGGCACCGTCATGCGGCAGGG\n+CTACCAACTGGGTGAGCAGGTGCTGCGGCACGCCTTGGTCGGCGTCGTCGACACGGTGGT\n+CGTCGACGCGGCCGAACTGGAGTCAGTCGACGACGGCACTGCGGTCGCAGATACCGCCGA\n+AAACGATCAAGCTGACCAGGGCAATAGCGCCGACACCTCGGGCGAACAGGCAGAATCAGA\n+ACCGTCGGGCAGTTAACAACAAAAGAGGAAGGCGAGAGGGGGTGACGCGACATGGCCCAA\n+AGGGAATGGGTCGAAAAAGACTTCTACCAGGAGCTGGGCGTCTCCTCTGATGCCAGTCCT\n+GAAGAGATCAAACGTGCCTATCGGAAGTTGGCGCGCGACCTGCATCCGGACGCGAACCCG\n+GGCAACCCGGCCGCCGGCGAACGGTTCAAGGCGGTTTCGGAGGCGCATAACGTGCTGTCG\n+GATCCGGCCAAGCGCAAGGAGTACGACGAAACCCGCCGCCTGTTCGCCGGCGGCGGGTTC\n+GGCGGCCGTCGGTTCGACAGCGGCTTTGGGGGCGGGTTCGGCGGTTTCGGGGTCGGTGGA\n+GACGGCGCCGAGTTCAACCTCAACGACTTGTTCGACGCCGCCAGCCGAACCGGCGGTACC\n+ACCATCGGTGACTTGTTCGGTGGCTTGTTCGGACGCGGTGGCAGCGCCCGTCCCAGCCGC\n+CCGCGACGCGGCAACGACCTGGAGACCGAGACCGAGTTGGATTTCGTGGAGGCCGCCAAG\n+GGCGTGGCGATGCCGCTGCGATTAACCAGCCCGGCGCCGTGCACCAACTGCCATGGCAGC\n+GGGGCCCGGCCAGGCACCAGCCCAAAGGTGTGTCCCACTTGCAACGGGTCGGGCGTGATC\n+AACCGCAATCAGGGCGCGTTCGGCTTCTCCGAGCCGTGCACCGACTGCCGAGGTAGCGGC\n+TCGATCATCGAGCACCCCTGCGAGGAGTGCAAAGGCACCGGCGTGACCACCCGCACCCGA\n+ACCATCAACGTGCGGATCCCGCCCGGTGTCGAGGATGGGCAGCGCATCCGGCTAGCCGGT\n+CAGGGCGAGGCCGGGTTGCGCGGCGCTCCCTCGGGGGATCTCTACGTGACGGTGCATGTG\n+CGGCCCGACAAGATCTTCGGCCGCGACGGCGACGACCTCACCGTCACCGTTCCGGTCAGC\n+TTCACCGAATTGGCTTTGGGCTCGACGCTGTCGGTGCCTACCCTGGACGGCACGGTCGGG\n+GTCCGGGTGCCCAAAGGCACCGCTGACGGCCGCATTCTGCGTGTGCGCGGACGCGGTGTG\n+CCCAAGCGCAGTGGGGGTAGCGGCGACCTACTTGTCACCGTGAAGGTGGCCGTGCCGCCC\n+AATTTGGCAGGCGCCGCTCAGGAAGCTCTGGAAGCCTATGCGGCGGCGGAGCGGTCCAGT\n+GGTTTCAACCCGCGGGCCGGATGGGCAGGTAATCGCTGATGGCGAAGAACCCAAAGGACG\n+GGGAATCCCGGACGTTTTTGATCTCGGTAGCCGCCGAGCTAGCCGGCATGCATGCACAGA\n+CCCTGCGTACCTACGATCGTCTTGGGTTGGTCAGCCCGCGGCGCACCTCCGGTGGCGGG'..b'ATCGTCAGCGAGCGAGTATCCCAGGGCAGA\n+TTCTGGGCTTGGGCGGCACAAGATCGCCGCTTGGCGCGGTGCCCGACGCCGGCCACCGGT\n+GTGCGCGGGCCTGCAATGGGCGGTGGTGGGCGGTTGGCACCGTCGGGTTCGGCGCTGCCA\n+AATACCCCGAACAGCGAAGCGAATACCGCATCGAACGTGGCCAGTTCGTCTACACGGCTG\n+ACCAGGGTCAACCGCGCGCCCCAATACAGCGCCGCCGGCGTACGCGGCACCAACTGCTGC\n+AACGCCTGCACCAAACTCGCTTGACCGCTGGCGGACACCGGTATCCCGGCGTCGCGAAGG\n+CGCGCTGCCAGCGCTGCCGCGAACGCCGCGAGGTCGACGCCCGGCAACAGTGCAGGGGTG\n+GCCATCCCATTCATCGCCGCCGGCGCAGCACCCAGATCAGCAGCAGCACGGTCAGCGCCG\n+CCAGCAGCGCCGAACCGTACTTTTTGAGCTGGCCGCCGTCGGCCAGCTGCAGCAAGTCGA\n+TGGGCGCCGCTTCGGTAGCAGGGGGTGTGCCTTGCGGGCTTTCTGAACTCTGGGCCGCGA\n+GCTCGGCTTCTAGCGAATCCACGAACTGGCCCAGCAGCTTCTCCGACACCTGCTGCAGCA\n+TGCCACTGCCGAATTGCGCCAGTTTGCCGACAATCTTCAGATCGGTGTCGACGGTGACGC\n+GGGTACGCTCTCCGACCTCGTGCAGCTGGGCAGCGACCGTGGCGGCCGCGTTGCCGGTAC\n+CGCGCGCCTCCTTGCCTTTGGCGTCGAAAACGGCGCGGTGCTGGTTGCGGTCCTGCTCGA\n+CAAAGTGCACCTTGCCGCTGAACTCGCTGGTGACCGGCCCAACCTTGACCTTGACCTTAC\n+CGAGGTACTCGTCGCCCTCATGGCCGATCAACTGGGCTCCAGGCATCAGCGGAATCATCT\n+GCTCCAGGTCGCATAGCCTGCTCCAGGCCTGCTCGATCGGAGCGCTGACGGTGAACTCGT\n+TGGCGATCTTCATCCTGTGCGTCCTCTCATGCGTGGCTGCACTCAGTAAAAGCTTGGTAC\n+GCATCGCGAATCTGCGTACGGTCGTCGGGCGTTTTGGCCAGGGCCCCAAGGCTGGCCAGA\n+GCGGGACTCGAATCCGCTGCGGTGAGGTCTGCGACCCCGAGTGCCACCAAAGCCGCCACC\n+CAGTCGATAGTCTCGGCCACACCGGGTGGCTTGTCCAGATCGAGATCCCGTGCAGTGCAA\n+ACGAATTGAGTGGCGTTCTCGATCAACGGCGCGGTAGCCCCGGGCACCGTGCGGCGCACG\n+ATCGCGGCCGCCCGGTCCGGCCCCGGGTAGTCGATCCAGTGGTAGAGGCAGCGCCGCCGC\n+AGTGCGTCGTGCAGGTCACGGCTGCGGTTGGACGTGAGCACCGCGATCGGCGGGCACTCC\n+GCGAGGAAAGTGCCCAGCTCGGGAACGGTCACCGCGGACTCACCAAGGAACTCCAGCAGT\n+AACGCCTCGAATTCGTCGTCGGCCCGGTCGATTTCATCGATGAGCAGCACTGGAGGGGTC\n+GGTCCGCGGTGCCGCACGCACCGCAGGATGGGCCGGTCCACCAGATACGCCTCGGTGTAC\n+AGATCCGCTTCCGATATGTCTGAGATACCCTTGCCGCGCGCCTCGGCCAGCCTGATGGAC\n+AATAGCTGGCGTTGGTAGTTCCAGTCGTAGAGCGCCTCGTTGGCCGTCAGCCCTTCATAG\n+CATTGCAGCCGGATCAGCGTGGTATCCAACACGACTGCAAGGGTTTTCGCGGCTGTTGTC\n+TTGCCAACACCGGGCTCACCCTCCAACAACAGCGGCCTGCCCAGCGTAACCGCCAGATAG\n+ATTGCCGACGCCGTGCCGGTATCCAGCAGGTAGTTCTGTTCGTCGAACCGGCGGATCACG\n+TCGTCGGGACTTGCGAAGGTCACGAGGGCACCGATTCCAGCAGCCGTCGGTAGTCGTCCC\n+AGGTGTCCACGTCAAGCGGCACGCAGCCGTCCACGGCGAGTTCGCGCACTGGGTGGCGGC\n+CGGAGTGCACCAGCTTCCAGACACCCTTGTCGCCGTGCAGTCGCGCGAGTTCGCCGAACA\n+CGGTGCGGCTAAACCAGAATGGATGCCCGACGCCGTCGGCGTAGCGGCACACCATGATCT\n+CGGTGGCCGGCCCGACGTCGATGATCCGCCGCAGTGTCGCCGGCGCCACCTGAGGCTGGT\n+CGCCCAGCATCAGCACGATCCCGGTGGCCCGCGGATGCACCCGTGCCAACGCGACGCGCA\n+GCGATGCCGCACACCCGCGCTCGACATCCTCGACGACCACCACGTCGGTCCCGTCCAGCG\n+CCATCGCGGCACGCACCGCCGACGCCGCACCGCCCAGGGTGAGGATCAGCTGGTCGAATC\n+CGGCTTGCCGGGCAACGTCGAGGGTGGCCCCAAGCACCGTGGTATCCCGATATGGCAGTA\n+GCTGTTTGGGCGTGCCCAACCGGTTGGAGCGCCCGGCGGCGAGTACCACACCGGTGATCT\n+GGGTCGCGGTCATGCGCCGCCGTTCTCGTCCGCCAACGCCTTCCGGCCTCTGGGGCCGCC\n+GCCGCGCAGCGTGGCGATCAGTTCCGCCGCAATCGACACCGCGATCTCCGCCGGAGTTTT\n+GGCGCCGATGGCCAATCCGACCGGGGTATGCACCCGGGCCCGCTCGGCATCGGACAGGTC\n+CAGCGAATCCAGGATGGACGCGCCGCGTACCGTGCTGGCCACCAGCCCGACATACCCAAC\n+GCCGTTATCCAGCGCCGTGCGGATGATTTCGGCTTCGGGCCCGCCGTGGCTGGCGATCAC\n+AATCGCAGTTGGCAAGGCGTCGGTGTCGGCCGGATCGGTGTCGCGGCGCGCGTCGTAGCC\n+CAACAGGCCGCACAGTTCGATCAACGCGTCGGCGATCGGGGTTTCGCCGTAAATCTGGAT\n+CAGCGGGGCCGGCAGCTGCGGGGTCAGGAAGATCTCCAGGGATCCGCCGGCCAGGCACGG\n+GTTGACCACCACACACGCCCCGGGAGCTTCCGGGAAGTGCACGTCACCGTCGGGCAGCAC\n+GCGCAGCAGCACGCTCTCGCCGGCCTGCAACACGCCCATCGCCGCCTTGCGGACCGAGTT\n+CTGCGCGCAGTGGCCGCCGACAAAGCCCTCGATGGTGCCGTCCGCCAACAGGATTGCCTC\n+ATCGCCCGGGCGGGCCGACGTGGGCTGCTGGGCCCGCACCACGGTCGCGCGCACGAACGG\n+TGTCCGCGCGGCCACCAGCTGTGCGGCCCGGTCACTGATGGACATCGACGCCCTCGAGCT\n+CCCCTAGATCGGTGGTGTGGCCCGGCCCTGCATGGCCTCCCAGACCCGCGACGGCGTCAA\n+CGGCATGTCGGCGTGCCGAACCCCGAACGGCGCCAACGCATCCACCACCGCGTTCACCAC\n+CGCCGGCGGGGAACCCACCGTGGCCGACTCACCGATGCCCTTGGCGCCGATCGGGTGATG\n+CGGCGACGGGGTCACGGTGTGCCCGGTCTCTAGGTGTGGCACCTCGAGCGCGGTCGGGAT\n+CAGGTAGTCCATCAACGATCCGCCCAGACAGTTGCCGTCCTCGTCGAAGGCAATCATCTC\n+CATCAGCGCCATGCCGATGCCGTCGACGATGCCGCCGTGTACCTGACCCTCGATGATCAT\n+CGGGTTGATCCGGGTTCCGCAATCATCGACGGCCAAAAAGCGCCGCACCTTCACCACCGC\n+GGTGCCCGGGTCGATGTCGACCACACAGAAGTAGGCGCCGTACGGGTAGGTCAGATTCGA\n+CGGGTTGTAGCAGACCTCGGCATCCAGCCCGCCCTCGATGCCCTCGGGCAGATCGCCGGC\n+GCCGTGCGCGCGCATCGCGATGTCGGCGATGGTCACCGCGGCCGACGGGTCACCCTTGAC\n' 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