| Next changeset 1:cdcaa40e5e45 (2021-12-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/vcfanno/ commit d962b44c5d3fecd1a315d6fbda8831d6de1b2801" |
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added:
macros.xml test-data/ex.bam test-data/ex.bam.bai test-data/exac.vcf.gz test-data/fitcons.bed test-data/query.vcf.gz test-data/vcfanno_result.vcf vcfanno.xml |
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| diff -r 000000000000 -r fb20fa735dfe macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jan 21 10:33:49 2021 +0000 |
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| @@ -0,0 +1,69 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">0.3.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">vcfanno</requirement> + <requirement type="package">tabix</requirement> + <requirement type="package">samtools</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>vcfanno --help</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex">@online{vcfanno, + author = {Brent S. Pedersen}, + title = {vcfanno}, + year = 2016, + url = {https://github.com/brentp/vcfanno}, + urldate = {2020-12-03} + }</citation> + <citation type="doi">10.1186/s13059-016-0973-5</citation> + </citations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">vcfanno</xref> + </xrefs> + </xml> + + <!-- + Inputs + --> + <macro name = "ops"> + <option value="self" selected="true">self - pull directly from the annotation and handle multi-allelics</option> + <option value="concat">concat - comma delimited list of output</option> + <option value="count">count - count the number of overlaps</option> + <option value="div2">div2 - given two values a and b, return a / b</option> + <option value="first">first - take only the first value</option> + <option value="flag">flag - presense/absence via VCF flag</option> + <option value="max">max (numbers only)</option> + <option value="mean">mean (numbers only)</option> + <option value="min">min (numbers only)</option> + <option value="sum">sum (numbers only)</option> + <option value="uniq">uniq - comma-delimited list of uniq values</option> + <option value="by_alt">by_alt - comma-delimited by alt (Number=A), pipe-delimited (|) for multiple annos for the same alt.</option> + <yield/> + </macro> + + <!-- + Help + --> + + <token name="@WID@"><![CDATA[ +*vcfanno* allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. + + - For VCF, values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. + + - For BED, values are pulled from (1-based) column number. + + - For BAM, depth (count), "mapq" and "seq" are currently supported. + ]]></token> + <token name="@REFERENCES@"><![CDATA[ +More information are available in the `mailing list <https://groups.google.com/g/vcfanno>`_ and `github <https://github.com/brentp/vcfanno>`_. + ]]></token> +</macros> |
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| diff -r 000000000000 -r fb20fa735dfe test-data/fitcons.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fitcons.bed Thu Jan 21 10:33:49 2021 +0000 |
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| diff -r 000000000000 -r fb20fa735dfe test-data/vcfanno_result.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfanno_result.vcf Thu Jan 21 10:33:49 2021 +0000 |
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| b'@@ -0,0 +1,487 @@\n+##fileformat=VCFv4.1\n+##contig=<ID=1>\n+##contig=<ID=10>\n+##contig=<ID=11>\n+##contig=<ID=12>\n+##contig=<ID=13>\n+##contig=<ID=14>\n+##contig=<ID=15>\n+##contig=<ID=16>\n+##contig=<ID=17>\n+##contig=<ID=18>\n+##contig=<ID=19>\n+##contig=<ID=2>\n+##contig=<ID=20>\n+##contig=<ID=21>\n+##contig=<ID=22>\n+##contig=<ID=3>\n+##contig=<ID=4>\n+##contig=<ID=5>\n+##contig=<ID=6>\n+##contig=<ID=7>\n+##contig=<ID=8>\n+##contig=<ID=9>\n+##contig=<ID=GL000191.1>\n+##contig=<ID=GL000192.1>\n+##contig=<ID=GL000193.1>\n+##contig=<ID=GL000194.1>\n+##contig=<ID=GL000195.1>\n+##contig=<ID=GL000196.1>\n+##contig=<ID=GL000197.1>\n+##contig=<ID=GL000198.1>\n+##contig=<ID=GL000199.1>\n+##contig=<ID=GL000200.1>\n+##contig=<ID=GL000201.1>\n+##contig=<ID=GL000202.1>\n+##contig=<ID=GL000203.1>\n+##contig=<ID=GL000204.1>\n+##contig=<ID=GL000205.1>\n+##contig=<ID=GL000206.1>\n+##contig=<ID=GL000207.1>\n+##contig=<ID=GL000208.1>\n+##contig=<ID=GL000209.1>\n+##contig=<ID=GL000210.1>\n+##contig=<ID=GL000211.1>\n+##contig=<ID=GL000212.1>\n+##contig=<ID=GL000213.1>\n+##contig=<ID=GL000215.1>\n+##contig=<ID=GL000216.1>\n+##contig=<ID=GL000217.1>\n+##contig=<ID=GL000218.1>\n+##contig=<ID=GL000219.1>\n+##contig=<ID=GL000221.1>\n+##contig=<ID=GL000222.1>\n+##contig=<ID=GL000223.1>\n+##contig=<ID=GL000224.1>\n+##contig=<ID=GL000225.1>\n+##contig=<ID=GL000227.1>\n+##contig=<ID=GL000228.1>\n+##contig=<ID=GL000230.1>\n+##contig=<ID=GL000231.1>\n+##contig=<ID=GL000233.1>\n+##contig=<ID=GL000235.1>\n+##contig=<ID=GL000236.1>\n+##contig=<ID=GL000238.1>\n+##contig=<ID=GL000240.1>\n+##contig=<ID=GL000242.1>\n+##contig=<ID=GL000243.1>\n+##contig=<ID=GL000244.1>\n+##contig=<ID=GL000246.1>\n+##contig=<ID=GL000247.1>\n+##contig=<ID=GL000248.1>\n+##contig=<ID=GL000249.1>\n+##contig=<ID=MT>\n+##contig=<ID=X>\n+##contig=<ID=Y>\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">\n+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n+##INFO=<ID=AC_AFR,Number=A,Type=Integer,Description="African/African American Allele Counts (from input_0.vcf.gz)">\n+##INFO=<ID=AC_AMR,Number=A,Type=Integer,Description="American Allele Counts (from input_0.vcf.gz)">\n+##INFO=<ID=AC_EAS,Number=A,Type=Integer,Description="East Asian Allele Counts (from input_0.vcf.gz)">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">\n+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that \'=\' is replaced by \'M\' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">\n+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">\n+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">\n+##INFO=<ID=EFF,Number=.,Type=String,'..b'6471;AN=34;AO=101;CIGAR=1X;TYPE=snp;mapq=33.5;coverage=4;xdp2=4,0\tGT:DP:RO:QR:AO:QA:GL\t0/1:94:76:2505:18:295:-10,0,-10\t0/0:22:20:520:2:37:0,-0.744048,-10\t0/0:48:39:1379:9:107:-4.52401,0,-10\n+1\t94824\t.\tC\tT\t6727.2\t.\tAB=0.423369;ABP=36.6236;AC=17;AF=0.5;AN=34;AO=279;CIGAR=1X;TYPE=snp;mapq=33.5;coverage=4;xdp2=4,0\tGT:DP:RO:QR:AO:QA:GL\t0/1:107:78:2566:29:706:-10,0,-10\t0/1:26:19:535:7:195:-10,0,-10\t0/1:48:32:1112:16:437:-10,0,-10\n+1\t94861\t.\tG\tT\t35.0\t.\tAB=0.4;ABP=3.87889;AC=1;AF=0.0294118;AN=34;AO=6;CIGAR=1X;TYPE=snp;mapq=37;coverage=1;xdp2=1,0\tGT:DP:RO:QR:AO:QA:GL\t0/0:56:53:1764:0:0:0,-10,-10\t0/1:10:6:174:4:132:-10,0,-10\t0/0:24:21:714:0:0:0,-6.32163,-10\n+1\t94893\t.\tA\tG\t35.0\t.\tAB=1;ABP=11.6962;AC=1;AF=0.0357143;AN=28;AO=15;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/0:68:68:2470:0:0:0,-10,-10\t0/1:4:0:0:4:135:-10,-1.20412,0\t0/0:27:25:880:2:23:0,-3.3975,-10\n+1\t94991\t.\tG\tA\t683.9\t.\tAB=0.351351;ABP=17.2129;AC=2;AF=0.111111;AN=18;AO=26;CIGAR=1X;TYPE=snp;mapq=40.1429;coverage=7;xdp2=3,4\tGT:DP:RO:QR:AO:QA:GL\t0/1:74:48:1608:26:918:-10,0,-10\t.:.:.:.:.:.:.\t0/0:26:26:868:0:0:0,-7.82678,-10\n+1\t95006\t.\tA\tT\t1209.5\t.\tAB=0.274611;ABP=88.1703;AC=16;AF=0.470588;AN=34;AO=71;CIGAR=1X;TYPE=snp;mapq=39;coverage=2;xdp2=1,1\tGT:DP:RO:QR:AO:QA:GL\t0/0:86:83:2850:3:106:0,-10,-10\t0/1:4:0:0:4:152:-10,-1.20412,0\t0/1:33:29:1025:4:128:-6.51795,0,-10\n+1\t95011\t.\tT\tG\t674.6\t.\tAB=0.47619;ABP=3.94093;AC=12;AF=0.352941;AN=34;AO=111;CIGAR=1X1M;TYPE=snp;mapq=21.6667;coverage=3;xdp2=2,1\tGT:DP:RO:QR:AO:QA:GL\t0/0:84:79:2791:3:19:0,-10,-10\t0/1:10:3:49:6:64:-4.76644,0,-3.48501\t0/0:34:29:1054:3:26:0,-3.75548,-10\n+1\t95054\t.\tG\tA\t201.1\t.\tAB=0.25;ABP=24.725;AC=1;AF=0.0294118;AN=34;AO=10;CIGAR=1X;TYPE=snp;mapq=28.6667;coverage=3;xdp2=1,2\tGT:DP:RO:QR:AO:QA:GL\t0/0:85:85:2938:0:0:0,-10,-10\t0/0:16:16:558:0:0:0,-4.81648,-10\t0/0:49:49:1618:0:0:0,-10,-10\n+1\t95611\t.\tG\tA\t36.8\t.\tAB=0.235294;ABP=13.3567;AC=1;AF=0.0294118;AN=34;AO=4;CIGAR=1X;TYPE=snp;mapq=20;coverage=3;xdp2=3,0\tGT:DP:RO:QR:AO:QA:GL\t0/0:17:17:620:0:0:0,-5.11751,-10\t0/0:2:2:70:0:0:0,-0.60206,-6.65\t0/0:7:7:252:0:0:0,-2.10721,-10\n+1\t96594\t.\tC\tT\t953.0\t.\tAB=0.355556;ABP=19.3205;AC=2;AF=0.111111;AN=18;AO=32;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:90:58:2040:32:1200:-10,0,-10\t.:.:.:.:.:.:.\t0/0:18:18:623:0:0:0,-5.41854,-10\n+1\t97164\t.\tA\tG\t353.7\t.\tAB=0;ABP=0;AC=12;AF=1;AN=12;AO=12;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t1/1:3:0:0:3:102:-9.52,-0.90309,0\t.:.:.:.:.:.:.\t1/1:1:0:0:1:35:-3.5,-0.30103,0\n+1\t97587\t.\tG\tC\t303.7\t.\tAB=0.285714;ABP=19.7617;AC=1;AF=0.05;AN=20;AO=12;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/1:42:30:1120:12:451:-10,0,-10\t0/0:1:1:40:0:0:0,-0.30103,-4\t0/0:21:21:796:0:0:0,-6.32163,-10\n+1\t97661\t.\tT\tC\t33.4\t.\tAB=0.3;ABP=6.48466;AC=1;AF=0.0333333;AN=30;AO=5;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/0:19:18:629:1:41:0,-0.340816,-10\t0/0:2:2:74:0:0:0,-0.60206,-7.03\t0/0:8:8:292:0:0:0,-2.40824,-10\n+1\t97937\t.\tT\tA\t12.3\t.\tAB=0.428571;ABP=3.32051;AC=2;AF=0.0588235;AN=34;AO=5;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/0:26:26:899:0:0:0,-7.82678,-10\t0/0:3:3:113:0:0:0,-0.90309,-10\t0/0:7:7:248:0:0:0,-2.10721,-10\n+1\t97953\t.\tA\tG\t1000.6\t.\tAB=0.401709;ABP=12.8283;AC=13;AF=0.382353;AN=34;AO=48;CIGAR=1X;TYPE=snp;mapq=20.5;coverage=2;xdp2=2,0\tGT:DP:RO:QR:AO:QA:GL\t0/0:32:32:1102:0:0:0,-9.63296,-10\t0/1:6:4:155:2:77:-6.68491,0,-10\t0/0:10:10:355:0:0:0,-3.0103,-10\n+1\t98683\t.\tG\tA\t610.5\t.\tAB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp;AC_AFR=0;AC_AMR=0;AC_EAS=0\tGT:DP:RO:QR:AO:QA:GL\t0/0:73:71:2641:2:78:0,-10,-10\t0/0:1:0:0:1:34:-3.4,-0.30103,0\t0/1:33:29:1059:4:139:-7.53545,0,-10\n+1\t98688\t.\tG\t<DEL>\t610.5\t.\tCIEND=-4,2;SVLEN=10;AB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/0:73:71:2641:2:78:0,-10,-10\t0/0:1:0:0:1:34:-3.4,-0.30103,0\t0/1:33:29:1059:4:139:-7.53545,0,-10\n+2\t98688\t.\tG\t<DEL>\t610.5\t.\tCIEND=-4,2;SVLEN=10;AB=0.282443;ABP=56.8661;AC=11;AF=0.34375;AN=32;AO=45;CIGAR=1X;TYPE=snp\tGT:DP:RO:QR:AO:QA:GL\t0/0:73:71:2641:2:78:0,-10,-10\t0/0:1:0:0:1:34:-3.4,-0.30103,0\t0/1:33:29:1059:4:139:-7.53545,0,-10\n' |
| b |
| diff -r 000000000000 -r fb20fa735dfe vcfanno.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfanno.xml Thu Jan 21 10:33:49 2021 +0000 |
| [ |
| b'@@ -0,0 +1,266 @@\n+<?xml version="1.0"?>\n+<tool id="vcfanno" name="vcfanno" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>VCF annotation</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="xrefs"/>\n+\n+ <expand macro="requirements"/>\n+\n+ <expand macro="version_command"/>\n+\n+ <!--\n+ In future versions - figure out how to safely add in lua support without posing security risk\n+ (Should be doable but requires writing some lua unfortunately to make custom sandboxes)\n+ -->\n+ <command detect_errors="exit_code"><![CDATA[\n+ ln -s \'$config_toml\' config.toml &&\n+ ln -s \'$input_vcf\' input.vcf &&\n+\n+ #for $i, $annotation in enumerate($annotations):\n+ #set $ext = str($annotation.type.type_select)\n+ ln -s \'$annotation.type.annotation\' \'input_${i}.${ext}\' &&\n+ ### These sets of conversions etc shouldn\'t be necessary but the vcfanno in Galaxy looks for an index file regardless of compression for some reason and if not present fails.\n+ #if $ext == \'vcf\' or $ext == \'bed\':\n+ bgzip \'input_${i}.${ext}\' &&\n+ #set $ext = $ext + ".gz"\n+ #end if\n+ #if \'.gz\' in $ext[-3:]:\n+ tabix -p vcf \'input_${i}.${ext}\' &&\n+ #elif $ext == \'bam\':\n+ ln -s \'${annotation.type.annotation.metadata.bam_index}\' input_${i}.bam.bai &&\n+ #end if\n+ #end for\n+ vcfanno -p \\${GALAXY_SLOTS:-4}\n+#if $ends:\n+ \'$ends\'\n+#end if\n+#if $permissive_overlap:\n+ \'$permissive_overlap\'\n+#end if\n+ config.toml\n+ input.vcf\n+ >\n+ \'$out_vcf\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="config_toml">#\n+#for $i, $annotation in enumerate($annotations):\n+ #set $ext = $annotation.type.type_select\n+ #if $ext == \'vcf\' or $ext == \'bed\':\n+ #set $ext = $ext + ".gz"\n+ #end if\n+ #if $ext == \'vcf.gz\' or $ext == \'bam\':\n+ #set $annotation_names = list()\n+ #set $annotation_fields = list()\n+ #set $annotation_ops = list()\n+ #for $field in $annotation.type.fields:\n+ #silent $annotation_names.append(\'"%s"\' %(str($field.name)))\n+ #silent $annotation_fields.append(\'"%s"\' %(str($field.field)))\n+ #silent $annotation_ops.append(\'"%s"\' %(str($field.op)))\n+ #end for\n+ #set $names = "names= [%s]" % (", ".join($annotation_names))\n+ #set $fields = "fields= [%s]" % (", ".join($annotation_fields))\n+ #set $ops = "ops= [%s]" % (", ".join($annotation_ops))\n+ #elif $ext == \'bed.gz\':\n+ #set $annotation_names = list()\n+ #set $annotation_columns = list()\n+ #set $annotation_ops = list()\n+ #for $field in $annotation.type.fields:\n+ #silent $annotation_names.append(\'"%s"\' %(str($field.name)))\n+ #silent $annotation_columns.append( str($field.columns))\n+ #silent $annotation_ops.append(\'"%s"\' %(str($field.op)))\n+ #end for\n+ #set $names = "names= [%s]" % (", ".join($annotation_names))\n+ #set $fields = "columns= [%s]" % (", ".join($annotation_columns))\n+ #set $ops = "ops= [%s]" % (", ".join($annotation_ops))\n+ #end if \n+[[annotation]]\n+file="input_${i}.${ext}"\n+${names}\n+${fields}\n+${ops}\n+\n+#end for\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="input_vcf" type="data" format="vcf,vcf_bgzip" label="VCF to be annotated"/>\n+ <param argument="-ends" type="boolean" checked="false" truevalue="-ends" falsevalue="" label="annotate the start and end as well as the interval itself?"/>\n+ <param argument="-permissive-overlap" type="boolean" checked="false" truevalue="-permissive-overlap" falsevalue="" label="annotate with an overlapping variant even it doesn\'t share the same ref and alt alleles." help="Default is to require exact match between variants."/>\n+ <repeat name="annotations" title="Input annotations" min="1">\n+ <conditional '..b' <param name="field" value="AC_AFR" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="AC_AMR" />\n+ <param name="field" value="AC_AMR" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="AC_EAS" />\n+ <param name="field" value="AC_EAS" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="ID" />\n+ <param name="field" value="ID" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ </conditional>\n+ </repeat>\n+ <repeat name="annotations">\n+ <conditional name="type">\n+ <param name="type_select" value="bam" />\n+ <param name="annotation" value="ex.bam" />\n+ <repeat name="fields">\n+ <param name="name" value="mapq" />\n+ <param name="field" value="mapq" />\n+ <param name="op" value="mean" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="coverage" />\n+ <param name="field" value="coverage" />\n+ <param name="op" value="sum" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="xdp2" />\n+ <param name="field" value="DP2" />\n+ <param name="op" value="self" />\n+ </repeat>\n+ </conditional>\n+ </repeat>\n+ <repeat name="annotations">\n+ <conditional name="type">\n+ <param name="type_select" value="bed" />\n+ <param name="annotation" value="fitcons.bed" />\n+ <repeat name="fields">\n+ <param name="name" value="lua_start" />\n+ <param name="columns" value="4" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="lua_end" />\n+ <param name="columns" value="4" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="lua_len" />\n+ <param name="columns" value="4" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="lua_mean" />\n+ <param name="columns" value="4" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ <repeat name="fields">\n+ <param name="name" value="lua_loc" />\n+ <param name="columns" value="4" />\n+ <param name="op" value="first" />\n+ </repeat>\n+ </conditional>\n+ </repeat>\n+ <output name="out_vcf" file="vcfanno_result.vcf"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+@WID@\n+\n+Note this version of vcfanno does not support lua code functionality\n+\n+**Input**\n+\n+- VCF file to be annotated\n+\n+- BAM / BED / VCF files to annotate with\n+\n+**Output**\n+\n+- Annotated VCF\n+\n+**References**\n+\n+@REFERENCES@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |