| Previous changeset 8:53c0b7a1a0c3 (2020-04-07) Next changeset 10:77b2770508f6 (2021-02-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit ffcf3989e7b05726341bbd0457a2e58448361554" |
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modified:
minimap2.xml |
| b |
| diff -r 53c0b7a1a0c3 -r 8c6cd2650d1f minimap2.xml --- a/minimap2.xml Tue Apr 07 18:39:38 2020 -0400 +++ b/minimap2.xml Thu Jun 04 22:29:50 2020 -0400 |
| [ |
| b'@@ -1,13 +1,24 @@\n <?xml version="1.0"?>\n-<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy1" profile="17.01">\n+<tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy2" profile="17.01">\n <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>\n <macros>\n <token name="@TOOL_VERSION@">2.17</token>\n+ <xml name="pe_anaylsis_fixed_selector">\n+ <param name="analysis_type_selector" type="select"\n+ label="Presets for PE reads alignment"\n+ help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">\n+ <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>\n+ </param>\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>\n <requirement type="package" version="1.9">samtools</requirement>\n </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ <regex match="\\[ERROR\\]" source="stderr" level="fatal" />\n+ </stdio>\n <version_command>minimap2 --version</version_command>\n <command>\n <![CDATA[\n@@ -17,83 +28,108 @@\n ln -f -s \'$reference_source.ref_file.fields.path\' reference.fa &&\n #end if\n minimap2\n- #if str($analysis_type_selector) == \'self-homology\':\n+ #if str($fastq_input.analysis_type_selector) == \'self-homology\':\n -DP -k19 -w19 -m200\n- #else\n- -x $analysis_type_selector\n+ #elif $fastq_input.analysis_type_selector:\n+ -x ${fastq_input.analysis_type_selector}\n #end if\n+\n ## indexing options\n $indexing_options.H\n- #if $indexing_options.k:\n+ #if str($indexing_options.k):\n -k $indexing_options.k\n #end if\n- #if $indexing_options.w:\n+ #if str($indexing_options.w):\n -w $indexing_options.w\n #end if\n- #if $indexing_options.I:\n+ #if str($indexing_options.I):\n -I $indexing_options.I\n #end if\n+\n ## Mapping options\n- #if $mapping_options.f:\n+ #if str($mapping_options.f):\n -f $mapping_options.f\n #end if\n- #if $mapping_options.min_occ_floor:\n+ #if str($mapping_options.min_occ_floor):\n --min-occ-floor $min_occ_floor\n #end if\n- #if $mapping_options.g:\n+ #if str($mapping_options.g):\n -g $mapping_options.g\n #end if\n- #if $mapping_options.G:\n- -G $mapping_options.G\n- #end if\n- #if $mapping_options.F:\n- -F $mapping_options.F\n- #end if\n- #if $mapping_options.r:\n+ #if str($mapping_options.r):\n -r $mapping_options.r\n #end if\n- #if $mapping_options.n:\n+ #if str($mapping_options.n):\n -n $mapping_options.n\n #end if\n- #if $mapping_options.m:\n+ #if str($mapping_options.m):\n -m $mapping_options.m\n #end if\n+ #if str($mapping_options.max_chain_skip):\n+ --max-chain-skip $mapping_options.max_chain_skip\n+ #end if\n+ #if str($mapping_options.max_chain_iter):\n+ --max-chain-iter $mapping_options.max_chain_iter\n+ #end if\n $mapping_options.X\n- #if $mapping_options.p:\n+ #if str($mapping_options.p):\n -p $mapping_options.p\n #end if\n- #if $mapping_options.N:\n+ #if str($mapping_options.N):\n -N $mapping_options.N\n #end if\n+\n ## Alignment options\n- #if $alignment_options.A:\n+ #if str($alignment_options.splicing.splice_mode) == \'--splice\':\n+ --frag=no --splice\n+ #if str($alignment_options.splicing.G):\n+ -G $alignment_options.splicing.G\n+ #end if\n+ #if str($alignment_options.splicing.C):\n+ -C $alignment_options.splicing.C\n+ #end if\n+ #if $alignment_opt'..b'sion penalties above"\n+ help="-E; default=1"/>\n+ <param argument="-z" type="integer" min="0" optional="true"\n+ label="Z-drop threshold for truncating an alignment"\n+ help="Increase to improve the contiguity of alignments at the cost of poorer alignments in the middle. default=400" />\n+ <param name="z2" type="integer" min="0" optional="true"\n+ label="Z-drop threshold for reverse-complementing the query"\n+ help="Decrease to find small inversions at the cost of performance and false positives. default=200" />\n+ <param argument="-s" type="integer" min="0" optional="true"\n+ label="minimal peak DP alignment score" help="default=80"/>\n+ <param name="no_end_flt" type="boolean" falsevalue="--no-end-flt" truevalue="" checked="true"\n+ label="Filter seeds towards the ends of chains before performing base-level alignment?" />\n </section>\n <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">\n <param name="output_format" type="select" label="Select an output format">\n@@ -296,7 +404,6 @@\n <param name="fastq_input_selector" value="paired"/>\n <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="sr"/>\n <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />\n </test>\n <test>\n@@ -306,7 +413,6 @@\n <param name="fastq_input_selector" value="paired"/>\n <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>\n <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="sr"/>\n <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" />\n </test>\n <test>\n@@ -320,7 +426,6 @@\n <element name="reverse" value="bwa-mem-fastq2.fq" />\n </collection>\n </param>\n- <param name="analysis_type_selector" value="sr"/>\n <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" />\n </test>\n <test>\n@@ -333,6 +438,28 @@\n <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />\n </test>\n <test>\n+ <!-- test alignment options -->\n+ <param name="reference_source_selector" value="cached" />\n+ <param name="ref_file" value="bwa-mem-mt-genome"/>\n+ <param name="fastq_input_selector" value="single"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>\n+ <param name="analysis_type_selector" value="sr"/>\n+ <section name="alignment_options">\n+ <!-- the folowing settings correspond to the defaults for "sr"\n+ mode. The purpose is to check that all alignment params get\n+ parsed correctly. -->\n+ <param name="A" value="2" />\n+ <param name="B" value="8" />\n+ <param name="O" value="12" />\n+ <param name="O2" value="32" />\n+ <param name="E" value="2" />\n+ <param name="E2" value="1" />\n+ <param name="z" value="400" />\n+ <param name="s" value="40" />\n+ </section>\n+ <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />\n+ </test> \n+ <test>\n <!-- test paf output -->\n <param name="reference_source_selector" value="history" />\n <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />\n' |