# HG changeset patch
# User galaxyp
# Date 1550819611 18000
# Node ID 2c7df0077d287dee8b82c171d8fa45a86ff5f497
# Parent  a3a66063d460396dd4e413339560d815be57ead9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 380011a7d342f3c7a2780dfa841adca1f6df1d30

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
@@ -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",
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
@@ -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">
diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_dbsnp_genomic_mapping.sqlite
Binary file test-data/hg19_dbsnp_genomic_mapping.sqlite has changed
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
@@ -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
diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_dbsnp_variant_annotation.sqlite
Binary file test-data/hg19_dbsnp_variant_annotation.sqlite has changed
diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_genomic_mapping.sqlite
Binary file test-data/hg19_genomic_mapping.sqlite has changed
diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_variant_annotation.rdata
Binary file test-data/hg19_variant_annotation.rdata has changed
diff -r a3a66063d460 -r 2c7df0077d28 test-data/hg19_variant_annotation.sqlite
Binary file test-data/hg19_variant_annotation.sqlite has changed