--- a/idpassemble.xml	Fri Oct 06 15:00:48 2017 -0400
+++ b/idpassemble.xml	Thu Nov 02 14:15:13 2017 -0400
@@ -27,6 +27,15 @@
             -FilterAtGeneLevel 1
             #end if
             -SummarizeSources 1
+            
+            #if $AssignSourceHierarchy
+            -AssignSourceHierarchy '$AssignSourceHierarchy'
+            #end if
+            
+            #if $IsobaricSampleMapping
+            -IsobaricSampleMapping '$IsobaricSampleMapping'
+            #end if
+            
             #if len($input) > 1
                 -MergedOutputFilepath output
                 #for $i in $input
@@ -56,6 +65,8 @@
         <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." />
     </inputs>
     <outputs>
         <data format="idpdb" name="output" from_work_dir="output" />
@@ -92,6 +103,7 @@
             <param name="MinSpectraPerDistinctMatch" value="1" />
             <param name="MinSpectraPerDistinctPeptide" value="1" />
             <param name="MaxProteinGroupsPerPeptide" value="10" />
+            <param name="AssignSourceHierarchy" value="assembly.tsv" ftype="tabular" />
             <output name="output" file="201208-378803-cm-filtered.idpDB" compare="sim_size" delta="500000" />
         </test>
         <test>
@@ -105,12 +117,66 @@
             <param name="MaxProteinGroupsPerPeptide" value="10" />
             <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" />
         </test>
+        <test>
+            <param name="input" value="201208-378803-embeddedGenesAndQuantitation.idpDB" />
+            <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" />
+        </test>
     </tests>
     <help>
 <![CDATA[
 **What it does**
 
 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
+======  ===========
+
+*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
+=====  ===========
+
+
+**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
+===============================  ==========================
+
+*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
+=============================  ================================================================================
+
 ]]>
     </help>
     <citations>