--- a/gotohscan.xml	Thu Jul 02 12:06:30 2015 -0400
+++ b/gotohscan.xml	Sun Nov 12 06:10:23 2017 -0500
@@ -3,26 +3,21 @@
     <requirements>
         <requirement type="package" version="1.3">gotohscan</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:"  level="fatal" description="Error occurred. Please check Tool Standard Error"/>
-        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
-    </stdio>
     <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
-    <command><![CDATA[
-        GotohScan
+    <command detect_errors="aggressive"><![CDATA[
+GotohScan
+        -d '$dbase'
+        -q '$query'
         
-        -d $dbase
-        -q $query
-        
-        #if $split and $split is not None
+        #if $split
             --split $split
         #end if
         
-        #if $e and $e is not None
+        #if $e
             -e $e
         #end if
         
-        #if $p and $p is not None
+        #if $p
             -p $p
         #end if
         
@@ -31,17 +26,17 @@
         > 
         
         #if $o.value == '0'
-            $output0
+            '$output0'
         #elif $o.value == '1'
-            $output1
+            '$output1'
         #elif $o.value == '2'
-            $output2
+            '$output2'
         #elif $o.value == '3'
-            $output3
+            '$output3'
         #elif $o.value == '4'
-            $output4
+            '$output4'
         #elif $o.value == '5'
-            $output5
+            '$output5'
         #end if
     ]]></command>
     <inputs>
@@ -90,12 +85,14 @@
     </tests>
     <help>
 <![CDATA[
+
 **GotohScan** is a search tool that finds shorter sequences
 (usually genes) in large database sequences (chromosomes, genomes, ..)
 by computing all semi-global alignments.  Thus, the query sequence is
 never truncated or split into subsequences, but always mapped to the
 database over its complete length. The alignment is computed via the
 Gotoh-alignment algorithm using affine gap costs.
+
 ]]></help>
     <citations>
         <citation type="doi">10.1093/nar/gkn1084</citation>

--- a/tool_dependencies.xml	Thu Jul 02 12:06:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="gotohscan" version="1.3">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/GotohScan/GotohScan-1.3.tar.gz</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>GotohScan</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable name="GOTOHSCAN_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>