| Previous changeset 4:33454033cdf6 (2017-03-11) Next changeset 6:5296d26b0373 (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_roh.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 33454033cdf6 -r 45091d60320f bcftools_roh.xml --- a/bcftools_roh.xml Sat Mar 11 18:05:17 2017 -0500 +++ b/bcftools_roh.xml Thu Apr 13 17:41:53 2017 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> - <description>HMM model for detecting runs of autozygosity</description> + <description>HMM model for detecting runs of homo/autozygosity</description> <macros> <token name="@EXECUTABLE@">roh</token> <import>macros.xml</import> @@ -12,6 +12,7 @@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ +@PREPARE_REGIONS_FILE@ ## General section #set $section = $sec_general @PREPARE_AF_FILE@ @@ -39,6 +40,13 @@ #if $section.rec_rate: --rec-rate "${section.rec_rate}" #end if +#if $section.buffer_size: + #if $section.buffer_overlap: + --buffer-size "${section.buffer_size},${section.buffer_overlap}" + #else: + --buffer-size "${section.buffer_size}" + #end if +#end if ## HMM section #set $section = $sec_hmm @@ -54,10 +62,15 @@ #set $section = $sec_restrict @REGIONS@ @TARGETS@ +@SAMPLES@ + +#if str($output_type) in ('r','s'): + --output-type $output_type +#end if ## Primary Input/Outputs @INPUT_FILE@ -> "$output_file" +> '$output_file' ]]> </command> <inputs> @@ -65,6 +78,7 @@ <section name="sec_restrict" expanded="false" title="Restrict to"> <expand macro="macro_regions" /> <expand macro="macro_targets" /> + <expand macro="macro_samples" /> </section> <section name="sec_general" expanded="true" title="Roh General Options"> <expand macro="macro_sample" /> @@ -77,25 +91,53 @@ <param name="skip_indels" type="boolean" truevalue="--skip-indels" falsevalue="" label="Skip Indels" help="Skip indels as their genotypes are enriched for errors" /> <param name="genetic_map" type="data" format="data" label="Genetic Map" optional="True" help="Genetic map in IMPUTE2 format, single file or mask, where string "{CHROM}" is replaced with chromosome name" /> <param name="rec_rate" type="float" label="Rec Rate" optional="True" help="Constant recombination rate per bp" /> + <param name="buffer_size" type="integer" label="Sliding Buffer Size" optional="True"> + <help> +Use when the entire many-sample file cannot fit into memory. +The number of sites to keep in memory. +If negative, it is interpreted as the maximum memory to use, in MB. + </help> + </param> + <param name="buffer_overlap" type="integer" min="0" label="Sliding Buffer Overlap" optional="True"> + <help> +The number of overlapping sites for the sliding buffer. The default overlap is set to roughly 1% of the buffer size. + </help> + </param> </section> <section name="sec_hmm" expanded="true" title="HMM Options"> <param name="hw_to_az" type="float" label="Hw To Az" value="6.7e-8" optional="True" help="P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state" /> <param name="az_to_hw" type="float" label="Az To Hw" value="5e-9" optional="True" help="P(HW|AZ) transition probability from AZ to HW state" /> <param name="viterbi_training" type="boolean" truevalue="--viterbi-training" falsevalue="" label="Viterbi Training" help="Perform Viterbi training to estimate transition probabilities" /> </section> + <param name="output_type" type="select" optional="true" label="limit output"> + <option value="s">s:per-site</option> + <option value="r">r:regions</option> + </param> </inputs> <outputs> <data name="output_file" format="tabular"/> </outputs> <tests> - <!-- Need an actual test input file --> <test> - <param name="input_file" ftype="vcf" value="mpileup.vcf" /> - <param name="sample" value="HG00100" /> + <param name="input_file" ftype="vcf" value="roh.vcf" /> + <param name="AF_dflt" value="0.4" /> + <param name="GTs_only" value="30" /> <output name="output_file"> <assert_contents> - <has_text text="HG00100"/> - <has_text text="State "/> + <has_text_matching expression="ST\tsample\t1"/> + <has_text_matching expression="RG\tsample\t1"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="roh.vcf" /> + <param name="AF_dflt" value="0.4" /> + <param name="GTs_only" value="30" /> + <param name="output_type" value="r" /> + <output name="output_file"> + <assert_contents> + <not_has_text text="ST"/> + <has_text_matching expression="RG\tsample\t1"/> </assert_contents> </output> </test> |
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| diff -r 33454033cdf6 -r 45091d60320f macros.xml --- a/macros.xml Sat Mar 11 18:05:17 2017 -0500 +++ b/macros.xml Thu Apr 13 17:41:53 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 33454033cdf6 -r 45091d60320f test-data/csq.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.fa Thu Apr 13 17:41:53 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 33454033cdf6 -r 45091d60320f test-data/csq.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.gff3 Thu Apr 13 17:41:53 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 33454033cdf6 -r 45091d60320f test-data/csq.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/csq.vcf Thu Apr 13 17:41:53 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 33454033cdf6 -r 45091d60320f test-data/mpileup.ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.ref.fa Thu Apr 13 17:41:53 2017 -0400 |
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| @@ -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 33454033cdf6 -r 45091d60320f 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 17:41:53 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 4200 14 60 61 |
| b |
| diff -r 33454033cdf6 -r 45091d60320f test-data/mpileup.regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.regions.bed Thu Apr 13 17:41:53 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 99 110 |
| b |
| diff -r 33454033cdf6 -r 45091d60320f test-data/mpileup.regions.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.regions.tab Thu Apr 13 17:41:53 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +17 100 110 |
| b |
| diff -r 33454033cdf6 -r 45091d60320f test-data/roh.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/roh.vcf Thu Apr 13 17:41:53 2017 -0400 |
| b |
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| diff -r 33454033cdf6 -r 45091d60320f 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 17:41:53 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 |
| b |
| diff -r 33454033cdf6 -r 45091d60320f 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 17:41:53 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> |