# HG changeset patch
# User geert-vandeweyer
# Date 1411639271 14400
# Node ID 92207f2ec144a31c7ab31eab3bab9a208cb63e48
# Parent  61b6d523acd976a2d0f052d6be0e410a7aa518c8
Various Fixes and added tool_data_conf

diff -r 61b6d523acd9 -r 92207f2ec144 DC_Genotyper.xml
--- a/DC_Genotyper.xml	Thu Sep 25 05:36:54 2014 -0400
+++ b/DC_Genotyper.xml	Thu Sep 25 06:01:11 2014 -0400
@@ -52,7 +52,6 @@
                   <when value="history">
 			<param name="ownFile" type="data" format="vcf,bcf" label="Select a dbSNP file from history"/>
 		  </when>
-		 </param>
           	</conditional>
 		<param name="mincov" value="400" type="integer" label="Minimal Coverage Depth" />
 		<param name="ploidy" type="integer" value='10' label="Expected Sample Ploidy" />
@@ -60,7 +59,7 @@
 	
 	<outputs>
 		<data format='txt' name="output1" label="${tool.name} on ${on_string}: Allele Fraction Distributions"/>
-		<data format='vcf' name='output2' label="${tool.name} on ${on_string}: VCF file">
+		<data format='vcf' name='output2' label="${tool.name} on ${on_string}: VCF file" />
 	</outputs>
 <help>
 
diff -r 61b6d523acd9 -r 92207f2ec144 DC_Genotyper_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DC_Genotyper_indexes.loc.sample	Thu Sep 25 06:01:11 2014 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables the DC_Genotyper  
+#tool to locate genome files for use with twoBitToFa, and IGVtools. You will
+#need to supply these files and then create a DC_Genotyper.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The DC_Genotyper.loc
+#file has this format (white space characters are TAB characters):
+#
+#<unique_build_id>	<display_name>		<2bit_path;IGVtools_genome.path>
+#
+#for example:
+#
+#hg19	Human (Homo sapiens): hg19		/depot/data2/galaxy/twobit/hg19.2bit;/depot/data2/galaxy/igvtools/hg19.chrom.sizes
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+# your igvtools folder needs the following files: 
+#
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.chrom.sizes
+#
+# igv chrom.sizes files are tab delimited files. First column is chromosome name, second column is length. Additional columns are ignored. 
+# example genome files are included in the installation location of the package_igvtools repository. 
+
diff -r 61b6d523acd9 -r 92207f2ec144 DC_Genotyper_indexes.log.sample
--- a/DC_Genotyper_indexes.log.sample	Thu Sep 25 05:36:54 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#This is a sample file distributed with Galaxy that enables the DC_Genotyper  
-#tool to locate genome files for use with twoBitToFa, and IGVtools. You will
-#need to supply these files and then create a DC_Genotyper.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The DC_Genotyper.loc
-#file has this format (white space characters are TAB characters):
-#
-#<unique_build_id>	<display_name>		<2bit_path;IGVtools_genome.path>
-#
-#for example:
-#
-#hg19	Human (Homo sapiens): hg19		/depot/data2/galaxy/twobit/hg19.2bit;/depot/data2/galaxy/igvtools/hg19.chrom.sizes
-#
-#then your /depot/data2/galaxy/twobit/ directory
-#would need to contain the following 2bit files:
-#
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
-#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
-#
-# your igvtools folder needs the following files: 
-#
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.chrom.sizes
-#
-# igv chrom.sizes files are tab delimited files. First column is chromosome name, second column is length. Additional columns are ignored. 
-# example genome files are included in the installation location of the package_igvtools repository. 
-
diff -r 61b6d523acd9 -r 92207f2ec144 readme.rst
--- a/readme.rst	Thu Sep 25 05:36:54 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-BACKGROUND:
-
-DC_Genotyper stands for Deep-Coverage Genotyper, and is aimed at detecting low fraction SNPs (no indels) in high-ploidy (or pooled) samples with very high coverage. It is being developed at the University of Antwerp by Geert Vandeweyer. 
-
-METHOD:
-
-DC_Genotyper generates a background noise distributions on a per-sample basis, and uses these distrubutions to detect non-reference sites. For non-reference sites, Allele-specific distributions are used to estimate if an allele surpasses the background signal (e.g. A_to_G has different distribution as A_to_C, also reflected in Tr/Tv ratios). 
-
-LIMITATION:
-
-This is a very early version with several limitations. Current limitations are : no support for indels, no plotting of the noise-models, incorrect syntax in for multi-allelic sites in the VCF file.
-
-Any feedback is welcome
-
-
-INSTALLATION:
-
-After installation, complete the dbsnp.loc and dc_genotyper_indexes.loc files. DCG supports multithreading, but keep tests have shown that using more than 6-8 threads will lead to I/O bottlenecks. 
diff -r 61b6d523acd9 -r 92207f2ec144 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Sep 25 06:01:11 2014 -0400
@@ -0,0 +1,13 @@
+<!-- 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>
+    <!-- Locations of all index files under genome directory -->
+    <table name="DC_Genotyper_indexes" comment_char="#">
+        <columns>name,value, path</columns>
+        <file path="DC_Genotyper_indexes.loc" />
+    </table>
+    <table name="dbsnp_indexes" comment_char="#">
+        <columns>name,value, path</columns>
+        <file path="dbsnp_indexes.loc" />
+    </table>
+
+</tables>