From 96c3902556bb43b51ee1e1a4a0bcb882364a5b47 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 23 Feb 2013 14:09:53 -0600
Subject: [PATCH 1/4] Implement macro mechanism for tool config XML. This
 should allow for a drastic reduction in 'code' duplication across XML files
 in a tool repository or inside of an XML file (repeated blocks in different
 when statements for instance).

---
 lib/galaxy/tools/__init__.py | 84 +++++++++++++++++++++++++++++++++++-
 1 file changed, 82 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 9bcb58a5bfe..a58d8f92360 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -17,6 +17,7 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.template import fill_template
 from galaxy import util, jobs, model
 from galaxy.jobs import ParallelismInfo
+from copy import deepcopy
 from elementtree import ElementTree
 from parameters import *
 from parameters.grouping import *
@@ -520,7 +521,7 @@ class ToolBox( object ):
     def load_tool( self, config_file, guid=None, **kwds ):
         """Load a single tool from the file named by `config_file` and return an instance of `Tool`."""
         # Parse XML configuration file and get the root element
-        tree = util.parse_xml( config_file )
+        tree = self._load_and_preprocess_tool_xml( config_file )
         root = tree.getroot()
         # Allow specifying a different tool subclass to instantiate
         if root.find( "type" ) is not None:
@@ -704,7 +705,86 @@ class ToolBox( object ):
             rval = tools
 
         return rval
-    
+
+    def _load_and_preprocess_tool_xml(self, config_file):
+        tree = util.parse_xml(config_file)
+        root = tree.getroot()
+        macros_el = root.find('macros')
+        if not macros_el:
+            return tree
+        tool_dir = os.path.dirname(config_file)
+        macros = self._load_macros(macros_el, tool_dir)
+        # HACK for elementtree, newer implementations (etree/lxml) won't
+        # require this parent_map data structure but elementtree does not
+        # track parents or recongnize .find('..').
+        parent_map = dict((c, p) for p in tree.getiterator() for c in p)
+        for expand_el in root.findall('.//expand'):
+            macro_name = expand_el.get('macro')
+            macro_def = macros[macro_name]
+            self._xml_replace(expand_el, macro_def, parent_map)
+        return tree
+
+    def _load_macros(self, macros_el, tool_dir):
+        macros = {}
+        # Import macros from external files.
+        macros.update(self._load_imported_macros(macros_el, tool_dir))
+        # Load all directly defined macros.
+        macros.update(self._load_embedded_macros(macros_el, tool_dir))
+        return macros
+
+    def _load_embedded_macros(self, macros_el, tool_dir):
+        macros = {}
+
+        macro_els = []
+        if macros_el:
+            macro_els = macros_el.findall("macro")
+        for macro in macro_els:
+            macro_name = macro.get("name")
+            macros[macro_name] = self._load_macro_def(macro)
+
+        return macros
+
+    def _load_imported_macros(self, macros_el, tool_dir):
+        macros = {}
+
+        macro_import_els = []
+        if macros_el:
+            macro_import_els = macros_el.findall("import")
+        for macro_import_el in macro_import_els:
+            raw_import_path = macro_import_el.text
+            tool_relative_import_path = \
+                os.path.basename(raw_import_path)  # Sanitize this
+            import_path = \
+                os.path.join(tool_dir, tool_relative_import_path)
+            file_macros = self._load_macro_file(import_path, tool_dir)
+            macros.update(file_macros)
+
+        return macros
+
+    def _load_macro_file(self, path, tool_dir):
+        tree = util.parse_xml(path)
+        root = tree.getroot()
+        return self._load_macros(root, tool_dir)
+
+    def _load_macro_def(self, macro):
+        return list(macro.getchildren())
+
+    def _xml_replace(self, query, targets, parent_map):
+        #parent_el = query.find('..') ## Something like this would be better with newer xml library
+        parent_el = parent_map[query]
+        matching_index = -1
+        #for index, el in enumerate(parent_el.iter('.')):  ## Something like this for newer implementation
+        for index, el in enumerate(parent_el.getchildren()):
+            if el == query:
+                matching_index = index
+                break
+        assert matching_index >= 0
+        current_index = matching_index
+        for target in targets:
+            current_index += 1
+            parent_el.insert(current_index, deepcopy(target))
+        parent_el.remove(query)
+
 class ToolSection( object ):
     """
     A group of tools with similar type/purpose that will be displayed as a

From b741ce0d49ab2db80f668e090a5d6a7336a10405 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 23 Feb 2013 14:09:53 -0600
Subject: [PATCH 2/4] Extend tool config macro engine so that macros may be
 rendered inside other macros.

---
 lib/galaxy/tools/__init__.py | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index a58d8f92360..db32ab835bc 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -714,16 +714,24 @@ class ToolBox( object ):
             return tree
         tool_dir = os.path.dirname(config_file)
         macros = self._load_macros(macros_el, tool_dir)
-        # HACK for elementtree, newer implementations (etree/lxml) won't
-        # require this parent_map data structure but elementtree does not
-        # track parents or recongnize .find('..').
-        parent_map = dict((c, p) for p in tree.getiterator() for c in p)
-        for expand_el in root.findall('.//expand'):
-            macro_name = expand_el.get('macro')
-            macro_def = macros[macro_name]
-            self._xml_replace(expand_el, macro_def, parent_map)
+
+        self._expand_macros([root], macros)
         return tree
 
+    def _expand_macros(self, elements, macros):
+        for element in elements:
+            # HACK for elementtree, newer implementations (etree/lxml) won't
+            # require this parent_map data structure but elementtree does not
+            # track parents or recongnize .find('..').
+            parent_map = dict((c, p) for p in element.getiterator() for c in p)
+            for expand_el in element.findall('.//expand'):
+                macro_name = expand_el.get('macro')
+                macro_def = macros[macro_name]
+
+                # Recursively expand contained macros.
+                self._expand_macros(macro_def, macros)
+                self._xml_replace(expand_el, macro_def, parent_map)
+
     def _load_macros(self, macros_el, tool_dir):
         macros = {}
         # Import macros from external files.
@@ -785,6 +793,7 @@ class ToolBox( object ):
             parent_el.insert(current_index, deepcopy(target))
         parent_el.remove(query)
 
+
 class ToolSection( object ):
     """
     A group of tools with similar type/purpose that will be displayed as a

From e9dc68f0a61caeda26f5183d3db9e3ec4944d030 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 23 Feb 2013 14:09:53 -0600
Subject: [PATCH 3/4] Add ability to pass sub-blocks of XML to macros and
 corresponding ability to render those (via the new <yield /> tag) from
 macros.

---
 lib/galaxy/tools/__init__.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index db32ab835bc..6ecb0006535 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -726,7 +726,16 @@ class ToolBox( object ):
             parent_map = dict((c, p) for p in element.getiterator() for c in p)
             for expand_el in element.findall('.//expand'):
                 macro_name = expand_el.get('macro')
-                macro_def = macros[macro_name]
+                macro_def = deepcopy(macros[macro_name])  # deepcopy needed?
+
+                yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')]
+
+                expand_el_children = expand_el.getchildren()
+                macro_def_parent_map = \
+                    dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p)
+
+                for yield_el in yield_els:
+                    self._xml_replace(yield_el, expand_el_children, macro_def_parent_map)
 
                 # Recursively expand contained macros.
                 self._expand_macros(macro_def, macros)

From 05028a920fed000fa6ec43a85fadc1fed0d0ccab Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 23 Feb 2013 14:09:53 -0600
Subject: [PATCH 4/4] Rework some duplication out tophat wrappers using macros.
 This dmeonstrates how macros can reduce duplication inside a file (e.g. the
 dbKeyActions macro) and between files (e.g. the own_junctionsConditional
 macro).

---
 tools/ngs_rna/tophat2_wrapper.xml      | 165 +++++------------------
 tools/ngs_rna/tophat_color_wrapper.xml | 175 +++++++------------------
 tools/ngs_rna/tophat_macros.xml        |  72 ++++++++++
 tools/ngs_rna/tophat_wrapper.xml       | 165 +++++------------------
 4 files changed, 186 insertions(+), 391 deletions(-)
 create mode 100644 tools/ngs_rna/tophat_macros.xml

diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index 5733bbe4a6e..fb0f1d19bca 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -143,23 +143,12 @@
                 </param>
             </when>
         </conditional>
-        <conditional name="refGenomeSource">
-          <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-in genomes were created using default options">
-            <option value="indexed" selected="True">Use a built-in genome</option>
-            <option value="history">Use a genome from history</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-              <options from_data_table="tophat2_indexes">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No genomes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>
-          <when value="history">
-            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
-          </when>  <!-- history -->
-        </conditional>  <!-- refGenomeSource -->
+        <expand macro="refGenomeSourceConditional">
+          <options from_data_table="tophat2_indexes">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No genomes are available for the selected input dataset"/>
+          </options>
+        </expand>
         <conditional name="params">
             <param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
               <option value="preSet">Use Defaults</option>
@@ -182,17 +171,7 @@
               <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
               <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
               <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
-              <conditional name="indel_search">
-                  <param name="allow_indel_search" type="select" label="Allow indel search">
-                      <option value="Yes">Yes</option>
-                      <option value="No">No</option>
-                  </param>
-                  <when value="No"/>
-                  <when value="Yes">
-                     <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
-                     <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
-                  </when>
-              </conditional>
+              <expand macro="indel_searchConditional" />
     alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
               <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
               <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
@@ -201,40 +180,7 @@
               <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
           
               <!-- Options for supplying own junctions. -->
-              <conditional name="own_junctions">
-                  <param name="use_junctions" type="select" label="Use Own Junctions">
-                    <option value="No">No</option>
-                    <option value="Yes">Yes</option>
-                  </param>
-                  <when value="Yes">
-                      <conditional name="gene_model_ann">
-                         <param name="use_annotations" type="select" label="Use Gene Annotation Model">
-                            <option value="No">No</option>
-                            <option value="Yes">Yes</option>
-                         </param>
-                         <when value="No" />
-                         <when value="Yes">
-                           <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
-                         </when>
-                      </conditional>
-                      <conditional name="raw_juncs">
-                         <param name="use_juncs" type="select" label="Use Raw Junctions">
-                            <option value="No">No</option>
-                            <option value="Yes">Yes</option>
-                         </param>
-                         <when value="No" />
-                         <when value="Yes">
-                           <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
-                         </when>
-                      </conditional>
-                      <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
-                        <option value="No">No</option>
-                        <option value="Yes">Yes</option>
-                      </param>
-                  </when>
-                  <when value="No" />
-              </conditional> <!-- /own_junctions -->
-          
+              <expand macro="own_junctionsConditional" />
               <!-- Coverage search. -->
               <conditional name="coverage_search">
                 <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
@@ -319,83 +265,40 @@
             <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
         </data>
         <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+            <expand macro="dbKeyActions" />
         </data>
         <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+          <expand macro="dbKeyActions" />
         </data>
         <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+          <expand macro="dbKeyActions" />
         </data>
         <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+          <expand macro="dbKeyActions" />
         </data>
     </outputs>
-
+    <macros>
+      <import>tophat_macros.xml</import>
+      <macro name="dbKeyActions">
+        <actions>
+          <conditional name="refGenomeSource.genomeSource">
+            <when value="indexed">
+              <action type="metadata" name="dbkey">
+                <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
+                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                </option>
+              </action>
+            </when>
+            <when value="history">
+              <action type="metadata" name="dbkey">
+                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+              </action>
+            </when>
+          </conditional>
+        </actions>
+      </macro>
+    </macros>
     <tests>
         <!-- Test base-space single-end reads with pre-built index and preset parameters -->
         <test>
diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml
index 72c0a277b29..399d2c9c46c 100644
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -154,23 +154,12 @@
     </command>
     <inputs>
         <param format="fastqcssanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Color-space: Must have Sanger-scaled quality values with ASCII offset 33" />
-        <conditional name="refGenomeSource">
-          <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
-            <option value="indexed">Use a built-in index</option>
-            <option value="history">Use one from the history</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-              <options from_data_table="tophat_indexes_color">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>
-          <when value="history">
-            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
-          </when>  <!-- history -->
-        </conditional>  <!-- refGenomeSource -->
+        <expand macro="refGenomeSourceConditional">
+          <options from_data_table="tophat_indexes_color">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+          </options>
+        </expand>
         <conditional name="singlePaired">
             <param name="sPaired" type="select" label="Is this library mate-paired?">
               <option value="single">Single-end</option>
@@ -194,17 +183,7 @@
                   <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
                   <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
-                  <conditional name="indel_search">
-                      <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="Yes">Yes</option>
-                          <option value="No">No</option>
-                      </param>
-                      <when value="No"/>
-                      <when value="Yes">
-                         <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
-                         <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
-                      </when>
-                  </conditional>
+                  <expand macro="indel_searchConditional" />
                   <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
                   <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
@@ -230,20 +209,8 @@
                                <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
                              </when>
                           </conditional>
-                          <conditional name="raw_juncs">
-                             <param name="use_juncs" type="select" label="Use Raw Junctions">
-                                <option value="No">No</option>
-                                <option value="Yes">Yes</option>
-                             </param>
-                             <when value="No" />
-                             <when value="Yes">
-                               <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
-                             </when>
-                          </conditional>
-                          <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
-                            <option value="No">No</option>
-                            <option value="Yes">Yes</option>
-                          </param>
+                          <expand macro="raw_juncsConditional" />
+                          <expand macro="no_novel_juncsParam" />
                       </when>
                       <when value="No" />
                   </conditional> <!-- /own_junctions -->
@@ -301,17 +268,7 @@
                   <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
                   <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
-                  <conditional name="indel_search">
-                      <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="Yes">Yes</option>
-                          <option value="No">No</option>
-                      </param>
-                      <when value="No"/>
-                      <when value="Yes">
-                         <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
-                         <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
-                      </when>
-                  </conditional>
+                  <expand macro="indel_searchConditional" />
                   <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
                   <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
@@ -399,90 +356,50 @@
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
                 ) 
             </filter>
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+            <expand macro="dbKeyActions" />
         </data>
         <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
-            <filter>
+            <expand macro="dbKeyActions" />            
+        </data>
+        <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
+            <expand macro="dbKeyActions" />
+        </data>
+        <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
+            <expand macro="dbKeyActions" />
+        </data>        
+    </outputs>
+    <macros>
+      <import>tophat_macros.xml</import>
+      <macro name="bedFilter">
+        <filter>
                 (
                     ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and 
                       ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or 
                     ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and 
                       ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
                 )
-            </filter>
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
-        </data>
-        <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
-        </data>
-        <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
-        </data>
-    </outputs>
+        </filter>        
+      </macro>
+      <macro name="dbKeyActions">
+        <actions>
+          <conditional name="refGenomeSource.genomeSource">
+            <when value="indexed">
+              <action type="metadata" name="dbkey">
+                <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
+                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                </option>
+              </action>
+            </when>
+            <when value="history">
+              <action type="metadata" name="dbkey">
+                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+              </action>
+            </when>
+          </conditional>
+        </actions>
+      </macro>
+    </macros>    
     <tests>
         <!-- Test color-space single-end reads with user-supplied reference fasta and preset parameters -->
         <test>
diff --git a/tools/ngs_rna/tophat_macros.xml b/tools/ngs_rna/tophat_macros.xml
new file mode 100644
index 00000000000..51ebec16d9a
--- /dev/null
+++ b/tools/ngs_rna/tophat_macros.xml
@@ -0,0 +1,72 @@
+<macros>
+  <macro name="refGenomeSourceConditional">
+    <conditional name="refGenomeSource">
+      <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
+        <option value="indexed" selected="True">Use a built-in genome</option>
+        <option value="history">Use a genome from history</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+          <yield />
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+      </when>  <!-- history -->
+    </conditional>  <!-- refGenomeSource -->
+  </macro>
+  <macro name="indel_searchConditional">
+    <conditional name="indel_search">
+      <param name="allow_indel_search" type="select" label="Allow indel search">
+        <option value="Yes">Yes</option>
+        <option value="No">No</option>
+      </param>
+      <when value="No"/>
+      <when value="Yes">
+        <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
+        <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
+      </when>
+    </conditional>    
+  </macro>
+  <macro name="own_junctionsConditional">
+    <conditional name="own_junctions">
+      <param name="use_junctions" type="select" label="Use Own Junctions">
+        <option value="No">No</option>
+        <option value="Yes">Yes</option>
+      </param>
+      <when value="Yes">
+        <conditional name="gene_model_ann">
+          <param name="use_annotations" type="select" label="Use Gene Annotation Model">
+            <option value="No">No</option>
+            <option value="Yes">Yes</option>
+          </param>
+          <when value="No" />
+          <when value="Yes">
+            <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
+          </when>
+        </conditional>
+        <expand macro="raw_juncsConditional" />
+        <expand macro="no_novel_juncsParam" />
+      </when>
+      <when value="No" />
+    </conditional> <!-- /own_junctions -->
+  </macro>
+  <macro name="raw_juncsConditional">
+    <conditional name="raw_juncs">
+      <param name="use_juncs" type="select" label="Use Raw Junctions">
+        <option value="No">No</option>
+        <option value="Yes">Yes</option>
+      </param>
+      <when value="No" />
+      <when value="Yes">
+        <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
+      </when>
+    </conditional>
+  </macro>
+  <macro name="no_novel_juncsParam">
+    <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
+      <option value="No">No</option>
+      <option value="Yes">Yes</option>
+    </param>
+  </macro>    
+</macros>
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 234040bc664..83321cdb9d5 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -151,23 +151,12 @@
     </command>
     <inputs>
         <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
-        <conditional name="refGenomeSource">
-          <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
-            <option value="indexed" selected="True">Use a built-in genome</option>
-            <option value="history">Use a genome from history</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-              <options from_data_table="tophat_indexes">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No genomes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>
-          <when value="history">
-            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
-          </when>  <!-- history -->
-        </conditional>  <!-- refGenomeSource -->
+        <expand macro="refGenomeSourceConditional">
+          <options from_data_table="tophat_indexes">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No genomes are available for the selected input dataset"/>
+          </options>
+        </expand>
         <conditional name="singlePaired">
             <param name="sPaired" type="select" label="Is this library mate-paired?">
               <option value="single">Single-end</option>
@@ -298,17 +287,7 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
                   <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
                   <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
                   <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
-                  <conditional name="indel_search">
-                      <param name="allow_indel_search" type="select" label="Allow indel search">
-                          <option value="Yes">Yes</option>
-                          <option value="No">No</option>
-                      </param>
-                      <when value="No"/>
-                      <when value="Yes">
-                         <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
-                         <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
-                      </when>
-                  </conditional>
+                  <expand macro="indel_searchConditional" />
                   <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
                   <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
                   <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
@@ -316,40 +295,7 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
                   <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
                   <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
                   <!-- Options for supplying own junctions. -->
-                  <conditional name="own_junctions">
-                      <param name="use_junctions" type="select" label="Use Own Junctions">
-                        <option value="No">No</option>
-                        <option value="Yes">Yes</option>
-                      </param>
-                      <when value="Yes">
-                          <conditional name="gene_model_ann">
-                             <param name="use_annotations" type="select" label="Use Gene Annotation Model">
-                                <option value="No">No</option>
-                                <option value="Yes">Yes</option>
-                             </param>
-                             <when value="No" />
-                             <when value="Yes">
-                               <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
-                             </when>
-                          </conditional>
-                          <conditional name="raw_juncs">
-                             <param name="use_juncs" type="select" label="Use Raw Junctions">
-                                <option value="No">No</option>
-                                <option value="Yes">Yes</option>
-                             </param>
-                             <when value="No" />
-                             <when value="Yes">
-                               <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
-                             </when>
-                          </conditional>
-                          <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
-                            <option value="No">No</option>
-                            <option value="Yes">Yes</option>
-                          </param>
-                      </when>
-                      <when value="No" />
-                  </conditional> <!-- /own_junctions -->
-                  
+                  <expand macro="own_junctionsConditional" />
                   <!-- Closure search. -->
                   <conditional name="closure_search">
                     <param name="use_search" type="select" label="Use Closure Search">
@@ -387,83 +333,40 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
 
     <outputs>
         <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+            <expand macro="dbKeyActions" />
         </data>
         <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+            <expand macro="dbKeyActions" />
         </data>
         <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+            <expand macro="dbKeyActions" />
         </data>
         <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
-            <actions>
-              <conditional name="refGenomeSource.genomeSource">
-                <when value="indexed">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
-                      <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                      <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                    </option>
-                  </action>
-                </when>
-                <when value="history">
-                  <action type="metadata" name="dbkey">
-                    <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                  </action>
-                </when>
-              </conditional>
-            </actions>
+            <expand macro="dbKeyActions" />
         </data>
     </outputs>
-
+    <macros>
+      <import>tophat_macros.xml</import>
+      <macro name="dbKeyActions">
+        <actions>
+          <conditional name="refGenomeSource.genomeSource">
+            <when value="indexed">
+              <action type="metadata" name="dbkey">
+                <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
+                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                </option>
+              </action>
+            </when>
+            <when value="history">
+              <action type="metadata" name="dbkey">
+                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+              </action>
+            </when>
+          </conditional>
+        </actions>
+      </macro>
+    </macros>
     <tests>
         <!-- Test base-space single-end reads with pre-built index and preset parameters -->
         <test>