# HG changeset patch
# User galaxyp
# Date 1453762815 18000
# Node ID 4c77cf5a29776ad961ca132434b92d54f7f95ba0
# Parent  663ee21a86090609e1dd288a380a63441d1e9a09
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

diff -r 663ee21a8609 -r 4c77cf5a2977 data_manager/customProDB_annotation.xml
--- a/data_manager/customProDB_annotation.xml	Thu Jan 21 18:19:52 2016 -0500
+++ b/data_manager/customProDB_annotation.xml	Mon Jan 25 18:00:15 2016 -0500
@@ -15,7 +15,7 @@
         </param>
         <param type="text" name="sequence_name" value="" label="Name of sequence" />
         <param type="text" name="sequence_id" value="" label="ID for sequence" />-->
-        <param type="text" name="dbkey" value="" label="UCSC dbKey for reference genome" />
+        <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
diff -r 663ee21a8609 -r 4c77cf5a2977 tool-data/customProDB.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/customProDB.loc.sample	Mon Jan 25 18:00:15 2016 -0500
@@ -0,0 +1,18 @@
+#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):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#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
+#
+#Your all_fasta.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.
+#
diff -r 663ee21a8609 -r 4c77cf5a2977 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Jan 25 18:00:15 2016 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all customProDB annotations under genome directory -->
+    <table name="customProDB" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/customProDB.loc" />
+    </table>
+</tables>