# HG changeset patch
# User galaxyp
# Date 1464104846 14400
# Node ID a0ca66b327928b51185d4b71a6f112cee5d74ac7
# Parent  b42974daa6599b5ce798ebcbf5af372c1276fc77
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty

diff -r b42974daa659 -r a0ca66b32792 COPYING
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Tue May 24 11:47:26 2016 -0400
@@ -0,0 +1,121 @@
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diff -r b42974daa659 -r a0ca66b32792 data_manager/customProDB_annotation.R
--- a/data_manager/customProDB_annotation.R	Thu Jan 28 18:46:50 2016 -0500
+++ b/data_manager/customProDB_annotation.R	Tue May 24 11:47:26 2016 -0400
@@ -16,6 +16,8 @@
 
 option_list <- list()
 option_list$dbkey <- make_option('--dbkey', type='character')
+option_list$dbsnp <- make_option('--dbsnp', type='character')
+option_list$cosmic <- make_option('--cosmic', type='logical')
 option_list$outputFile <- make_option('--outputFile', type='character')
 option_list$dbkey_description <- make_option('--dbkey_description', type='character')
 
@@ -24,6 +26,8 @@
 
 customProDB_annotation <- function(
 	dbkey = GalaxyCharacterParam(required=TRUE), 
+	dbsnp_str = GalaxyCharacterParam(required=FALSE), 
+	cosmic = GalaxyLogicalParam(required=FALSE), 
 	dbkey_description = GalaxyCharacterParam(required=FALSE), 
 	outputFile = GalaxyOutput("output","json"))
 {
@@ -37,6 +41,24 @@
         dbkey_description = dbkey
     }
 
+    if (length(dbsnp_str) > 0)
+    {
+        dbsnp = dbsnp_str
+    }
+    else
+    {
+        dbsnp = NULL
+    }
+    
+    if (cosmic && grepl("^hg", dbkey))
+    {
+        use_cosmic = TRUE
+    }
+    else
+    {
+        use_cosmic = NULL
+    }
+
     suppressPackageStartupMessages(library(rjson))
     params = fromJSON(file=outputFile)
     target_directory = params$output_data[[1]]$extra_files_path
@@ -65,7 +87,7 @@
     download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
 
     cat(paste("Preparing Refseq annotation files\n"))
-    customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory)
+    customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory, dbsnp=dbsnp, cosmic=use_cosmic)
     
     outputPath = paste(dbkey, "/customProDB", sep="")
     output = list(data_tables = list())
diff -r b42974daa659 -r a0ca66b32792 data_manager/customProDB_annotation.xml
--- a/data_manager/customProDB_annotation.xml	Thu Jan 28 18:46:50 2016 -0500
+++ b/data_manager/customProDB_annotation.xml	Tue May 24 11:47:26 2016 -0400
@@ -3,6 +3,10 @@
     <command interpreter="Rscript --vanilla">customProDB_annotation.R
       --outputFile "${out_file}"
       --dbkey "${dbkey}"
+      --dbsnp "${dbsnp}"
+      #if $cosmic
+            --cosmic true
+      #end if
       --dbkey_description ${ dbkey.get_display_text() }
       2&gt;&amp;1
     </command>
@@ -12,6 +16,8 @@
     </stdio>
     <inputs>
         <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
+        <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
+        <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
diff -r b42974daa659 -r a0ca66b32792 tool-data/customProDB.loc.sample
--- a/tool-data/customProDB.loc.sample	Thu Jan 28 18:46:50 2016 -0500
+++ b/tool-data/customProDB.loc.sample	Tue May 24 11:47:26 2016 -0400
@@ -1,18 +1,16 @@
 #This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
+#under the "customProDB" directory (a subdirectory of a genome build).
+#This file has the format (white space characters are TAB characters):
 #
-#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#<unique_build_id>	<dbkey>		<display_name>	<path to annotation files>
 #
 #So, all_fasta.loc could look something like this:
 #
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19full
 #
-#Your all_fasta.loc file should contain an entry for each individual
+#Your customProDB.loc file should contain an entry for each individual
 #fasta file. So there will be multiple fasta files for each build,
 #such as with hg19 above.
 #