# HG changeset patch
# User yhoogstrate
# Date 1446713102 18000
# Node ID c1424388f08b02ca8b9376dd1bde7cfb829b2a5f
# Parent  ddbaf017720aceaef749b36c931ed8412fa3fb30
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty

diff -r ddbaf017720a -r c1424388f08b samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml	Wed Nov 19 10:02:46 2014 -0500
+++ b/samtools-parallel-mpileup.xml	Thu Nov 05 03:45:02 2015 -0500
@@ -2,7 +2,7 @@
 <tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup" version="0.1.19a.a">
 	<description>Samtools mpileup (supporting parallelization)</description>
 	<requirements>
-		<requirement type="package" version="5.9">ncurses</requirement>
+		<requirement type="package" version="6.0">ncurses</requirement>
 		<requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement>
 		<requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
 	</requirements>
@@ -268,4 +268,12 @@
 
 http://testtoolshed.g2.bx.psu.edu/
 </help>
+	<citation type="bibtex">
+	   @unpublished{samtools_parallel_mpileup,
+		  author       = {Youri Hoogstrate}, 
+		  title        = { Samtools parallel-mpileup, fork of classical samtools },
+		  year         = 2014,
+		  url          = { https://github.com/yhoogstrate/parallel-mpileup }
+		}
+	</citation>
 </tool>
\ No newline at end of file
diff -r ddbaf017720a -r c1424388f08b tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 19 10:02:46 2014 -0500
+++ b/tool_dependencies.xml	Thu Nov 05 03:45:02 2015 -0500
@@ -1,55 +1,50 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<!--
-	<package name="ncurses" version="5.9">
-		<repository name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" />
-	</package>
-	-->
-	
-	<package name="ncurses" version="5.9">
-		<repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
-		
-	<package name="samtools" version="0.1.19">
-		<repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
-	
-	<package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a">
-		<install version="1.0">
-			<actions>
-				<action type="set_environment_for_install">
-					<repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-						<package name="ncurses" version="5.9" />
-					</repository>
-				</action>
-				
-				<action type="shell_command">
-				svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
-				
-				cd samtools-parallel-mpileup ;
-				cd $(ls |grep samtools-) ;
-				
-				sed -i 's/-lcurses/-lncurses/' Makefile ;
-                sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
-				
-				make ;
-				cp samtools ../samtools-parallel-mpileup</action>
-				<action type="move_file">
-					<source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
-					<destination>$INSTALL_DIR/bin</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-					<environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
-		</readme>
-	</package>
-	
-	<package name="varscan" version="2.3.6">
-		<repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
+    <package name="ncurses" version="6.0">
+        <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ncurses" version="5.9" />
+                    </repository>
+                </action>
+                
+                <action type="shell_command">
+                    svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ;
+                    
+                    cd samtools-parallel-mpileup ;
+                    cd $(ls |grep samtools-) ;
+                    
+                    sed -i 's/-lcurses/-lncurses/' Makefile ;
+                    sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ;
+                    
+                    make ;
+                    cp samtools ../samtools-parallel-mpileup
+                </action>
+                <action type="move_file">
+                    <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
+        </readme>
+    </package>
+    
+    <package name="varscan" version="2.3.6">
+        <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
 </tool_dependency>
diff -r ddbaf017720a -r c1424388f08b varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml	Wed Nov 19 10:02:46 2014 -0500
+++ b/varscan_mpileup2snp.xml	Thu Nov 05 03:45:02 2015 -0500
@@ -4,6 +4,9 @@
 	<requirements>
 		<requirement type="package" version="2.3.6">varscan</requirement>
 	</requirements>
+	
+	<version_command>java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&amp;1 | head -n 1</version_command>
+	
 	<command>
 		cat $mpileup_input | java
 			 -Xmx64G
@@ -26,7 +29,7 @@
 		#end if
 		
 		 2> stderr.txt 
-		 > $snv_output ;
+		  > $snv_output ;
 		 cat stderr.txt
 	</command>
 	
@@ -123,4 +126,7 @@
 
 http://testtoolshed.g2.bx.psu.edu/
 </help>
+    <citations>
+        <citation type="doi">10.1101/gr.129684.111</citation>
+    </citations>
 </tool>
\ No newline at end of file
diff -r ddbaf017720a -r c1424388f08b varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Nov 19 10:02:46 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Thu Nov 05 03:45:02 2015 -0500
@@ -323,4 +323,7 @@
 
 http://testtoolshed.g2.bx.psu.edu/
 </help>
+    <citations>
+        <citation type="doi">10.1101/gr.129684.111</citation>
+    </citations>
 </tool>
\ No newline at end of file