--- a/idpassemble.xml	Fri Nov 03 14:31:39 2017 -0400
+++ b/idpassemble.xml	Tue Nov 21 13:19:10 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="idpassemble" name="idpAssemble" version="@VERSION@.1">
+<tool id="idpassemble" name="idpAssemble" version="@VERSION@.0">
     <description>Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels.</description>
     <macros>
         <import>macros.xml</import>
@@ -28,12 +28,12 @@
             #end if
             -SummarizeSources 1
             
-            #if $AssignSourceHierarchy
-            -AssignSourceHierarchy '$AssignSourceHierarchy'
+            #if $AssignSourceHierarchyCondition.HasAssignSourceHierarchy
+            -AssignSourceHierarchy '$AssignSourceHierarchyCondition.AssignSourceHierarchy'
             #end if
             
-            #if $IsobaricSampleMapping
-            -IsobaricSampleMapping '$IsobaricSampleMapping'
+            #if $IsobaricSampleMappingCondition.HasIsobaricSampleMapping
+            -IsobaricSampleMapping '$IsobaricSampleMappingCondition.IsobaricSampleMapping'
             #end if
             
             #if len($input) > 1
@@ -65,8 +65,23 @@
         <param argument="-MinSpectraPerDistinctMatch" type="integer" label="Min Filtered Spectra per Distinct Match" min="1" value="1" help="Distinct matches with fewer than this number of spectra will be excluded from the filtered data set." />
         <param argument="-MinSpectraPerDistinctPeptide" type="integer" label="Min Filtered Spectra per Distinct Peptide" min="1" value="1" help="Distinct peptides with fewer than this number of spectra will be excluded from the filtered data set." />
         <param argument="-MaxProteinGroupsPerPeptide" type="integer" label="Max Protein Groups per Distinct Peptide" min="0" value="10" help="Peptides that map to more than this number of protein groups will be excluded from the filtered data set. Highly ambiguous peptides are not very useful for quantitation." />
-        <param argument="-AssignSourceHierarchy" type="data" format="tabular" optional="true" label="Assign source files to groups" help="A tab-delimited file that organizes source files (e.g. individual runs in a fractionated experiment) into groups. See below for more details." />
-        <param argument="-IsobaricSampleMapping" type="data" format="tabular" optional="true" label="Assign sample names to reporter ions" help="A tab-delimited file that gives sample names to isobaric reporter ion channels (i.e. iTRAQ, TMT) across a given source group. See below for more details." />
+
+        <conditional name="AssignSourceHierarchyCondition">
+            <param name="HasAssignSourceHierarchy" type="boolean" truevalue="1" falsevalue="0" label="Assign sources to a hierarchy?"/>
+            <when value="1">
+                <param argument="-AssignSourceHierarchy" type="data" format="tabular" optional="true" label="Assign source files to groups" help="A tab-delimited file that organizes source files (e.g. individual runs in a fractionated experiment) into groups. See below for more details." />
+            </when>
+            <when value="0">
+            </when>
+        </conditional>
+        <conditional name="IsobaricSampleMappingCondition">
+            <param name="HasIsobaricSampleMapping" type="boolean" truevalue="1" falsevalue="0" label="Assign sample names to reporter ions?"/>
+            <when value="1">
+                <param argument="-IsobaricSampleMapping" type="data" format="tabular" optional="true" label="Assign sample names to reporter ions" help="A tab-delimited file that gives sample names to isobaric reporter ion channels (i.e. iTRAQ, TMT) across a given source group. See below for more details." />
+            </when>
+            <when value="0">
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="idpdb" name="output" from_work_dir="output" />
@@ -103,6 +118,7 @@
             <param name="MinSpectraPerDistinctMatch" value="1" />
             <param name="MinSpectraPerDistinctPeptide" value="1" />
             <param name="MaxProteinGroupsPerPeptide" value="10" />
+            <param name="HasAssignSourceHierarchy" value="1" />
             <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
             <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" />
         </test>
@@ -119,6 +135,8 @@
         </test>
         <test>
             <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" />
+            <param name="HasAssignSourceHierarchy" value="1" />
+            <param name="HasIsobaricSampleMapping" value="1" />
             <param name="IsobaricSampleMapping" value="mapping.tsv" ftype="tabular" />
             <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
             <output name="output" file="201208-378803-embeddedGenesAndQuantitationWithMapping.idpDB" compare="sim_size" delta="500000" />
@@ -130,52 +148,63 @@
 
 Merges and filters one or more IDPicker 3 idpDB files into a combined idpDB file. Protein assembly (e.g. parsimony) is conducted on the combined set of proteins.
 
+====
 
 **AssignSourceHierarchy**
+
 The assembly file is a tab-delimited file with two columns that organizes the sources (individual runs) into a hierarchy.
 The first column is the name of a source group, the second column is the source path or name to assign to that group.
 A forward slash in the group name adds another level to the hierarchy (just like a directory path).
 
 *A simple example:*
-======  ===========
-/repA   repA1.idpDB
-/repA   repA2.idpDB
-/repB   repB1.idpDB
-/repB   repB2.idpDB
-======  ===========
+
+::
+
+/repA	repA1.idpDB
+/repA	repA2.idpDB
+/repB	repB1.idpDB
+/repB	repB2.idpDB
+
 
 *A multi-level example:*
-=====  ===========
-/A/1   A1_f1
-/A/1   A1_f2
-/A/2   A2_f1
-/A/2   A2_f2
-/B/1   B1_f1
-/B/1   B1_f2
-/B/2   B2_f1
-/B/2   B2_f2
-=====  ===========
+
+::
 
+/A/1	A1_f1
+/A/1	A1_f2
+/A/2	A2_f1
+/A/2	A2_f2
+/B/1	B1_f1
+/B/1	B1_f2
+/B/2	B2_f1
+/B/2	B2_f2
+
+====
 
 **IsobaricSampleMapping**
+
 The mapping file is a tab-delimited file with two columns. The first column is the full path to a source group,
 the second column is a comma-delimited list of sample names, in ascending order of reporter ion mass. The special
 sample name *Reference*, if present, will be used to normalize the other channels. Samples named *Empty* will be
 ignored.
 
+
 *iTRAQ-4plex example:*
-===============================  ==========================
-/Case/Group1_A123_B456_C789      A123,B456,C789,Reference
-/Case/Group2_D123_E456_F789      D123,E456,F789,Reference
-/Control/Group3_X123_Y456_Z789   Reference,X123,Y456,Z789
-/Control/Group4_U123_V456        U123,Reference,V456,Empty
-===============================  ==========================
+
+::
+
+/Case/Group1_A123_B456_C789	A123,B456,C789,Reference
+/Case/Group2_D123_E456_F789	D123,E456,F789,Reference
+/Ctrl/Group3_X123_Y456_Z789	Reference,X123,Y456,Z789
+/Ctrl/Group4_U123_V456_None	U123,Reference,V456,Empty
+
 
 *TMT-10plex example:*
-=============================  ================================================================================
-/Group1_Cases1-4_Controls1-4   Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference
-/Group2_Cases5-8_Controls5-8   Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference
-=============================  ================================================================================
+
+::
+
+/Group1_Cases1-4_Controls1-4	Case1,Case2,Case3,Case4,Reference,Control1,Control2,Control3,Control4,Reference
+/Group2_Cases5-8_Controls5-8	Case5,Case6,Case7,Case8,Reference,Control5,Control6,Control7,Control8,Reference
 
 ]]>
     </help>