# HG changeset patch
# User lparsons
# Date 1351281428 14400
# Node ID 971e20519fb89481a67c97bbb84790bda089d730
# Parent  5bfb7a651fac09d40141a0ef58739a01c39643df
Fix for dbkey column check when output additional bam is selected

diff -r 5bfb7a651fac -r 971e20519fb8 htseq-count.xml
--- a/htseq-count.xml	Fri Sep 21 17:57:47 2012 -0400
+++ b/htseq-count.xml	Fri Oct 26 15:57:08 2012 -0400
@@ -79,7 +79,7 @@
                     <when value="cached">
                         <param name="ref_file" type="select" label="Using reference genome">
                             <options from_data_table="sam_fa_indexes">
-                                <filter type="data_meta" key="dbkey" ref="samfile" column="3"/>
+                                <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
                             </options>
                             <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                         </param>
diff -r 5bfb7a651fac -r 971e20519fb8 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 21 17:57:47 2012 -0400
+++ b/tool_dependencies.xml	Fri Oct 26 15:57:08 2012 -0400
@@ -1,58 +1,58 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="numpy" version="1.6.2">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-
-    <package name="htseq" version="0.5.3p9">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
-        </readme>
-    </package>
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
-    </package>
-</tool_dependency>
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="numpy" version="1.6.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+
+    <package name="htseq" version="0.5.3p9">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
+        </readme>
+    </package>
+    <package name="samtools" version="0.1.18">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
+                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>misc/maq2sam-long</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Compiling SAMtools requires the ncurses and zlib development libraries.
+        </readme>
+    </package>
+</tool_dependency>