From 63fec8c3326e2e46114ea8a7e3ab04d7f390d203 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 6 Jun 2012 15:27:59 -0400
Subject: [PATCH] Add preset alignment options to Bowtie2 wrapper and fix
 default in Tophat2 wrapper.

---
 tools/ngs_rna/tophat2_wrapper.xml    |  4 ++--
 tools/sr_mapping/bowtie2_wrapper.py  | 10 ++++++++--
 tools/sr_mapping/bowtie2_wrapper.xml | 26 ++++++++++++++++++++++++++
 3 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index 32f6ed9f9d2..d59cf92b8be 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -281,8 +281,8 @@
                           <when value="Yes">
                               <param name="b2_preset_select" type="select" label="Preset option">
                                   <option value="very-fast">Very fast</option>
-                                  <option selected="true" value="fast">Fast</option>
-                                  <option value="sensitive">Sensitive</option>
+                                  <option value="fast">Fast</option>
+                                  <option selected="true" value="sensitive">Sensitive</option>
                                   <option value="very-sensitive">Very sensitive</option>
                               </param>
                           </when>
diff --git a/tools/sr_mapping/bowtie2_wrapper.py b/tools/sr_mapping/bowtie2_wrapper.py
index 0a3d8690a6d..b82acc4bf03 100644
--- a/tools/sr_mapping/bowtie2_wrapper.py
+++ b/tools/sr_mapping/bowtie2_wrapper.py
@@ -19,9 +19,12 @@ def __main__():
     parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
     parser.add_option( '', '--single-paired', dest='single_paired', help='' )
     parser.add_option( '', '--settings', dest='settings', help='' )
+    parser.add_option( '', '--end-to-end', dest='end_to_end', action="store_true" )
+    parser.add_option( '', '--local', dest='local', action="store_true" )
+    parser.add_option( '', '--preset-alignment', dest='preset_alignment')
 
     (options, args) = parser.parse_args()
-
+    
     # Creat bowtie index if necessary.
     tmp_index_dir = tempfile.mkdtemp()
     if options.own_file:
@@ -73,7 +76,10 @@ def __main__():
     if options.settings == 'preSet':
         pass
     else:
-        pass
+        if options.local:
+            opts += ' --local'
+        if options.preset_alignment:
+            opts += " --" + options.preset_alignment
         
     # Final command:
     cmd = cmd % ( opts, index_path, reads, options.output )
diff --git a/tools/sr_mapping/bowtie2_wrapper.xml b/tools/sr_mapping/bowtie2_wrapper.xml
index a3a4c82e090..4e26d8437c0 100644
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -34,6 +34,12 @@
 
         ## Set params.
         --settings=$params.settingsType
+        
+        #if str($params.align_type) == "end_to_end":
+            --end-to-end --preset-alignment=$params.preset.align_preset_select
+        #else:
+            --local --preset-alignment=$params.preset.align_preset_select-local
+        #end if
     </command>
     <inputs>
         <conditional name="singlePaired">
@@ -75,6 +81,26 @@
             <when value="preSet" />
             <!-- Full/advanced params. -->
             <when value="full">
+                <param name="align_type" type="select" label="Type of alignment">
+                    <option selected="true" value="end_to_end">End to end</option>
+                    <option value="local">Local</option>
+                </param>
+                <conditional name="preset">
+                    <param name="b2_preset" type="select" label="Use Preset options">
+                          <option selected="true" value="Yes">Yes</option>
+                          <option value="No">No</option>
+                    </param>
+                    <when value="Yes">
+                        <param name="align_preset_select" type="select" label="Preset option">
+                            <option value="very-fast">Very fast</option>
+                            <option value="fast">Fast</option>
+                            <option selected="true" value="sensitive">Sensitive</option>
+                            <option value="very-sensitive">Very sensitive</option>
+                        </param>
+                    </when>
+                    <!-- TODO: -->
+                    <when value="No" />
+                </conditional>
             </when>  <!-- full -->
       </conditional>  <!-- params -->
     </inputs>