| Previous changeset 5:a3a66063d460 (2017-11-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 380011a7d342f3c7a2780dfa841adca1f6df1d30 |
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modified:
customProDB.R customProDB.xml test-data/hg19_dbsnp_variant_annotation.sqlite test-data/hg19_genomic_mapping.sqlite test-data/hg19_variant_annotation.rdata test-data/hg19_variant_annotation.sqlite |
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added:
test-data/hg19_dbsnp_genomic_mapping.sqlite |
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removed:
test-data/hg19_dbsnp_variant_annotation.rdata |
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| diff -r a3a66063d460 -r 2c7df0077d28 customProDB.R --- a/customProDB.R Wed Nov 01 19:33:53 2017 -0400 +++ b/customProDB.R Fri Feb 22 02:13:31 2019 -0500 |
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| @@ -100,9 +100,9 @@ file.symlink(bai_file, paste(bamLink, ".bai", sep="")) # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) - download.file("https://github.com/chambm/customProDB/archive/9db2223ef9932e50124b92d1bc49206af1f40fb3.zip", "customProDB.zip", quiet=TRUE) + download.file("https://github.com/chambm/customProDB/archive/13cbebf9e3f26507afbbb661c9e985da2fd0840a.zip", "customProDB.zip", quiet=TRUE) unzip("customProDB.zip") - devtools::load_all("customProDB-9db2223ef9932e50124b92d1bc49206af1f40fb3") + devtools::load_all("customProDB-13cbebf9e3f26507afbbb661c9e985da2fd0840a") easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", |
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| diff -r a3a66063d460 -r 2c7df0077d28 customProDB.xml --- a/customProDB.xml Wed Nov 01 19:33:53 2017 -0400 +++ b/customProDB.xml Fri Feb 22 02:13:31 2019 -0500 |
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| @@ -1,25 +1,16 @@ -<tool id="custom_pro_db" name="CustomProDB" version="1.16.1.0"> +<tool id="custom_pro_db" name="CustomProDB" version="1.22.0"> <description>Generate protein FASTAs from exosome or transcriptome data</description> <requirements> - <requirement type="package" version="3.3.1">r-base</requirement> - <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>--> - <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> - <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> - <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement> - <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement> - <requirement type="package" version="1.11.1">r-devtools</requirement> - <requirement type="package" version="3.98_1.4">r-xml</requirement> - <requirement type="package" version="0.10.11">r-rmysql</requirement> - <requirement type="package" version="1.0.2">r-testthat</requirement> - <requirement type="package" version="0.1.0">r-getoptlong</requirement> - <requirement type="package" version="1.1.2">r-stringi</requirement> - <requirement type="package" version="1.1.0">r-stringr</requirement> - <requirement type="package" version="1.10.0">r-data.table</requirement> - <requirement type="package" version="0.4_10">r-sqldf</requirement> - <requirement type="package" version="0.6_6">r-gsubfn</requirement> - <requirement type="package" version="2.3_47">r-chron</requirement> - <requirement type="package" version="0.3_10">r-proto</requirement> + <!--<requirement type="package" version="1.22.0">bioconductor-customprodb</requirement>--> + <requirement type="package" version="1.26.0">bioconductor-rgalaxy</requirement> + <requirement type="package" version="1.28.3">bioconductor-variantannotation</requirement> + <requirement type="package" version="2.0.1">r-devtools</requirement> + <requirement type="package" version="2.0.1">r-testthat</requirement> + <requirement type="package" version="0.1.7">r-getoptlong</requirement> + <requirement type="package" version="1.12.0">r-data.table</requirement> + <requirement type="package" version="0.4_11">r-sqldf</requirement> <requirement type="package" version="1.8.4">r-plyr</requirement> + <requirement type="package" version="0.10.13">r-rmysql</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> @@ -161,7 +152,7 @@ <output name="output_rpkm" file="hg19_rpkm0.fasta" /> <output name="output_snv" file="hg19_dbsnp_snv.fasta" /> <output name="output_indel" file="hg19_indel.fasta" /> - <output name="output_variant_annotation_rdata" file="hg19_dbsnp_variant_annotation.rdata" /> + <output name="output_genomic_mapping_sqlite" file="hg19_dbsnp_genomic_mapping.sqlite" /> <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" /> </test> <test expect_num_outputs="3"> |
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| diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_dbsnp_genomic_mapping.sqlite |
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| Binary file test-data/hg19_dbsnp_genomic_mapping.sqlite has changed |
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| diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_dbsnp_variant_annotation.rdata --- a/test-data/hg19_dbsnp_variant_annotation.rdata Wed Nov 01 19:33:53 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ ->NP_000170_T139I,E956D |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 -MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPIRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLDKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_001120983_rs121913332:R1432* |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a -MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTK |
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| diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_dbsnp_variant_annotation.sqlite |
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| diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_genomic_mapping.sqlite |
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