| Previous changeset 5:0a564427739d (2017-03-11) Next changeset 7:b03984136ce4 (2017-12-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e |
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modified:
bcftools_call.xml macros.xml |
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added:
test-data/csq.fa test-data/csq.gff3 test-data/csq.vcf test-data/mpileup.1.bam test-data/mpileup.1.bam.bai test-data/mpileup.2.bam test-data/mpileup.2.bam.bai test-data/mpileup.3.bam test-data/mpileup.3.bam.bai test-data/mpileup.3.cram test-data/mpileup.4.bam test-data/mpileup.ref.fa test-data/mpileup.ref.fa.fai test-data/mpileup.regions.bed test-data/mpileup.regions.tab test-data/roh.vcf tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 0a564427739d -r 3296c3680d96 bcftools_call.xml --- a/bcftools_call.xml Sat Mar 11 17:57:29 2017 -0500 +++ b/bcftools_call.xml Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="1.3.2.0"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@"> <description>SNP/indel variant calling from VCF/BCF</description> <macros> <token name="@EXECUTABLE@">call</token> @@ -41,6 +41,8 @@ @PREPARE_TARGETS_FILE@ #end if #end if +#set $section = $sec_restrict +@PREPARE_REGIONS_FILE@ bcftools @EXECUTABLE@ @@ -50,6 +52,9 @@ #if str($section.gvcf) != '': --gvcf $section.gvcf #end if + #if str($section.prior_freqs) != '': + --prior-freqs $section.prior_freqs + #end if #if $section.genotypes.constrain == 'alleles': --constrain alleles $section.genotypes.insert_missed #set $section = $sec_consensus_variant_calling.variant_calling.genotypes @@ -104,7 +109,7 @@ ## Primary Input/Outputs @INPUT_FILE@ -> "$output_file" +> '$output_file' ]]> </command> <inputs> @@ -138,6 +143,17 @@ <expand macro="macro_novel_rate" /> </when> </conditional> + <param name="prior_freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> + <help> +<![CDATA[ +For example: --prior-freqs REF_AN,REF_AC +<br>if the input VCF has the following INFO tags: +<br>##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes"> +<br>##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele"> +]]> + </help> + <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator> + </param> <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" /> </when> <when value="consensus"> @@ -250,6 +266,7 @@ The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels. + @REGIONS_HELP@ @TARGETS_HELP@ |
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| diff -r 0a564427739d -r 3296c3680d96 macros.xml --- a/macros.xml Sat Mar 11 17:57:29 2017 -0500 +++ b/macros.xml Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">1.3.1</token> + <token name="@VERSION@">1.4.0</token> <xml name="stdio"> <stdio> <exit_code range="1:" /> @@ -10,12 +10,14 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="1.3.1">bcftools</requirement> - <!-- conda dependency --> - <requirement type="package" version="1.3.2">htslib</requirement> + <requirement type="package" version="1.4">bcftools</requirement> + <requirement type="package" version="1.4">htslib</requirement> <yield /> </requirements> </xml> + <xml name="samtools_requirement"> + <requirement type="package" version="1.3.1">samtools</requirement> + </xml> <xml name="version_command"> <version_command>bcftools 2>&1 | grep 'Version:'</version_command> </xml> @@ -245,7 +247,7 @@ </xml> <token name="@OUTPUT_TYPE@"> #if str($output_type) != "__none__": - --output-type "${output_type}" + --output-type '${output_type}' #end if </token> @@ -279,14 +281,30 @@ </when> </conditional> </xml> + <token name="@PREPARE_REGIONS_FILE@"> +<![CDATA[ +#set $regions_path = None +#if 'regions' in $section + #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: + #if $section.regions.regions_file.ext.startswith('bed'): + #set $regions_path = 'regions_file.bed' + ln -s '$section.regions.regions_file' $regions_path && + #end if + #end if +#end if +]]> + </token> <token name="@REGIONS@"> #if $section.regions.regions_src == 'regions' and $section.regions.regions != '': --regions '$section.regions.regions' #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: - --regions-file '$section.regions.regions_file' + #if $regions_path is not None: + --regions-file '$regions_path' + #else: + --regions-file '$section.regions.regions_file' + #end if #end if </token> - <xml name="macro_targets_file"> <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" > <yield/> @@ -356,11 +374,11 @@ <xml name="macro_samples"> <param name="samples" type="text" value="" label="Samples" optional="true" - help="(-s) comma separated list of samples to annotate (or exclude with "^" prefix)"> + help="(-s) comma separated list of samples to annotate (or exclude)"> <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> </param> <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" - help="inverts the query/filtering applied by Samples" /> + help="inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" /> <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" help="(-S) file of samples to include" /> <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" |
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| diff -r 0a564427739d -r 3296c3680d96 test-data/csq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.fa Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -0,0 +1,34 @@ +>1 +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +>2 +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +>3 +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT +ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT + |
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| diff -r 0a564427739d -r 3296c3680d96 test-data/csq.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.gff3 Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -0,0 +1,40 @@ +##gff-version 3 +#! This file shows which fields are used and required by `bcftools +csq`. It is a trimmed version +#! of the GFF3 format, see an example of the full format here +#! ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/ +#! +### +1 . gene 90 200 . + . ID=gene:ENSG00000000001;Name=XYZ;biotype=protein_coding +1 . transcript 90 200 . + . ID=transcript:ENST00000000001;Parent=gene:ENSG00000000001;biotype=protein_coding +1 . exon 90 110 . + . Parent=transcript:ENST00000000001 +1 . five_prime_UTR 90 98 . + . Parent=transcript:ENST00000000001 +1 . CDS 99 110 . + 1 Parent=transcript:ENST00000000001 +1 . exon 120 130 . + . Parent=transcript:ENST00000000001 +1 . CDS 120 130 . + 1 Parent=transcript:ENST00000000001 +1 . exon 140 150 . + . Parent=transcript:ENST00000000001 +1 . CDS 140 150 . + 2 Parent=transcript:ENST00000000001 +1 . exon 160 200 . + . Parent=transcript:ENST00000000001 +1 . CDS 160 171 . + 0 Parent=transcript:ENST00000000001 +1 . three_prime_UTR 172 200 . + . Parent=transcript:ENST00000000001 +2 . gene 80 200 . - . ID=gene:ENSG00000000002;Name=ABC;biotype=protein_coding +2 . transcript 80 200 . - . ID=transcript:ENST00000000002;Parent=gene:ENSG00000000002;biotype=protein_coding +2 . exon 80 110 . - . Parent=transcript:ENST00000000002 +2 . three_prime_UTR 80 98 . - . Parent=transcript:ENST00000000002 +2 . CDS 99 110 . - 0 Parent=transcript:ENST00000000002 +2 . exon 120 130 . - . Parent=transcript:ENST00000000002 +2 . CDS 120 130 . - 2 Parent=transcript:ENST00000000002 +2 . exon 140 150 . - . Parent=transcript:ENST00000000002 +2 . CDS 140 150 . - 1 Parent=transcript:ENST00000000002 +2 . exon 160 200 . - . Parent=transcript:ENST00000000002 +2 . CDS 160 171 . - 1 Parent=transcript:ENST00000000002 +2 . five_prime_UTR 172 200 . - . Parent=transcript:ENST00000000002 +3 . lincRNA_gene 20 50 . - . ID=gene:ENSG00000000004;Name=mir-007;biotype=lincRNA +3 . lincRNA 20 50 . - . ID=transcript:ENSG00000000004;Parent=gene:ENSG00000000004;biotype=lincRNA +3 . gene 100 200 . - . ID=gene:ENSG00000000003;Name=QWRTY;biotype=protein_coding +3 . transcript 100 200 . - . ID=transcript:ENST00000000003;Parent=gene:ENSG00000000003;biotype=protein_coding +3 . exon 100 110 . - . Parent=transcript:ENST00000000003 +3 . three_prime_UTR 100 105 . - . Parent=transcript:ENST00000000003 +3 . CDS 106 110 . - 0 Parent=transcript:ENST00000000003 +3 . exon 160 200 . - . Parent=transcript:ENST00000000003 +3 . CDS 160 171 . - 0 Parent=transcript:ENST00000000003 +3 . five_prime_UTR 172 200 . - . Parent=transcript:ENST00000000003 |
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| diff -r 0a564427739d -r 3296c3680d96 test-data/csq.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.vcf Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -0,0 +1,40 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence"> +##contig=<ID=1,length=2147483647> +##contig=<ID=2,length=2147483647> +##contig=<ID=3,length=2147483647> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SmplAAA SmplBBB +1 90 . C T . . EXP=5_prime_utr|XYZ|ENST00000000001|protein_coding GT 1|0 1|1 +1 102 . C T 1 . EXP=synonymous|XYZ|ENST00000000001|protein_coding|+|1Y|102C>T GT 1|0 1|0 +1 103 . G A 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2I|103G>A GT 1|0 0|0 +1 103 . G C 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2L|103G>C GT 0|0 1|0 +1 107 . G A 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|3R>3Q|107G>A+108T>A GT 1|0 1|0 +1 108 . T A 1 . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@107 GT 1|0 1|0 +1 121 . ACG A . . EXP=inframe_deletion|XYZ|ENST00000000001|protein_coding|+|5TY>5I|121ACG>A+124TA>T,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 1|0 +1 124 . TA T . . EXP=@121 GT 1|0 1|0 +1 128 . T C 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|7V>6A|128T>C+129A>C,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0/0 +1 129 . A C 1 . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@128 GT 1|0 0/0 +1 140 . TA AACG . . EXP=inframe_insertion|XYZ|ENST00000000001|protein_coding|+|8LR>7QRR|140TA>AACG+142C>CC,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0|0 +1 142 . C CC . . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@140 GT 1|0 0|0 +1 145 . AC TA . . EXP=stop_gained|XYZ|ENST00000000001|protein_coding|+|10T>10*|145AC>TA GT 1|0 0|0 +1 160 . TA T . . EXP=*frameshift|XYZ|ENST00000000001|protein_coding|+|12YVRT>12SYV|160TA>T,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0|0 +1 190 . C T . . EXP=3_prime_utr|XYZ|ENST00000000001|protein_coding GT 1|0 0|0 +2 97 . A C . . EXP=3_prime_utr|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +2 105 . AC A . . EXP=@121 GT 1|0 0|0 +2 121 . AC A . . EXP=frameshift|ABC|ENST00000000002|protein_coding|-|11VVRTY>11*|105AC>A+121AC>A,splice_region|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +2 126 . C CTT . . EXP=@127 GT 1|0 0|0 +2 127 . G GG . . EXP=inframe_insertion|ABC|ENST00000000002|protein_coding|-|9T>8TK|126C>CTT+127G>GG GT 1|0 0|0 +2 144 . TAC T . . EXP=@148 GT 1|0 0|0 +2 148 . TA T . . EXP=inframe_deletion|ABC|ENST00000000002|protein_coding|-|5YV>5T|144TAC>T+148TA>T,splice_region|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +2 164 . T G . . EXP=missense|ABC|ENST00000000002|protein_coding|-|3T>3P|164T>G GT 1|0 0|0 +2 165 . A C . . EXP=synonymous|ABC|ENST00000000002|protein_coding|-|2R|165A>C GT 1|0 0|0 +2 169 . A G . . EXP=@170 GT 1|0 0|0 +2 170 . C T . . EXP=missense|ABC|ENST00000000002|protein_coding|-|1V>1T|169A>G+170C>T GT 1|0 0|0 +2 199 . G T . . EXP=5_prime_utr|ABC|ENST00000000002|protein_coding GT 1|0 0|0 +3 20 . T A . . EXP=non_coding|mir-007||lincRNA GT 1|0 0|0 +3 109 . ACGTACGT A 1 . EXP=splice_acceptor|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 +3 113 . A T . . EXP=splice_region|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 +3 120 . T A . . EXP=intron|QWRTY||protein_coding GT 1|0 0|0 +3 152 . T A . . EXP=splice_region|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 +3 159 . G A . . EXP=splice_donor|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0 |
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| diff -r 0a564427739d -r 3296c3680d96 test-data/mpileup.ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.ref.fa Thu Apr 13 17:43:02 2017 -0400 |
| b |
| @@ -0,0 +1,71 @@ +>17 17:1-4200 +AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAA +TGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA +GCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAA +GACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACAC +GCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA +GTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGA +AAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATA +AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAG +GAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATC +ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTG +TGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT +GCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGG +CAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA +AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGA +TTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTAC +CAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG +TGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCG +CCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAA +GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGAC +CAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGT +TCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC +CCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC +GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCC +CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTA +GGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGA +GCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTT +TGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC +CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAG +CGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCA +CTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCC +TGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGG +TCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACA +GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC +CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCAC +GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGC +AGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGC +ACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCG +GCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAG +CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATC +GTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAA +AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGG +AGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCG +CATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAA +ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG +CCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCT +CTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT +TTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGG +ACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATG +TGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCT +TTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAG +CAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTG +CCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG +ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGG +GCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTA +ATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCA +GCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG +GCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGG +GAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGT +AAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCC +TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATAT +ATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTG +TTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTAC +ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGC +CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCG +TCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCAT +GCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAT +GGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCT +ACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATAT +TCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTT +CTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCAC |
| b |
| diff -r 0a564427739d -r 3296c3680d96 test-data/mpileup.ref.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.ref.fa.fai Thu Apr 13 17:43:02 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 4200 14 60 61 |
| b |
| diff -r 0a564427739d -r 3296c3680d96 test-data/mpileup.regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.regions.bed Thu Apr 13 17:43:02 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 99 110 |
| b |
| diff -r 0a564427739d -r 3296c3680d96 test-data/mpileup.regions.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.regions.tab Thu Apr 13 17:43:02 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 100 110 |
| b |
| diff -r 0a564427739d -r 3296c3680d96 test-data/roh.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/roh.vcf Thu Apr 13 17:43:02 2017 -0400 |
| b |
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| diff -r 0a564427739d -r 3296c3680d96 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
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| diff -r 0a564427739d -r 3296c3680d96 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Apr 13 17:43:02 2017 -0400 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |