--- a/assembly_post_processor.xml	Mon Jan 30 11:03:42 2017 -0500
+++ b/assembly_post_processor.xml	Tue Jan 31 11:10:35 2017 -0500
@@ -14,17 +14,17 @@
     <command>
         <![CDATA[
             AssemblyPostProcesser
-            --transcripts "$input"
+            --transcripts '$input'
             --prediction_method $prediction_method_cond.prediction_method
             #if str($prediction_method_cond.prediction_method) == 'estscan':
-                --score_matrices "$score_matrices"
+                --score_matrices '$score_matrices'
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-                    --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups"
-                    --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
-                    --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
-                    --method "$options_type.target_gene_family_assembly_cond.method"
+                    --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
+                    --scaffold_dir '${GALAXY_DATA_MANAGER_DATA_PATH}/plant_tribes/scaffolds'
+                    --scaffold '$options_type.target_gene_family_assembly_cond.scaffold'
+                    --method '$options_type.target_gene_family_assembly_cond.method'
                 #end if
                 --gap_trimming $options_type.gap_trimming
                 #if str($options_type.strand_specific) == 'yes':
@@ -98,12 +98,11 @@
         <test>
             <param name="input" value="assembly.fasta" ftype="fasta" />
             <param name="prediction_method" value="transdecoder" />
-            <param name="options_type_selector" value="basic" />
             <output_collection name="transcripts" type="list">
-                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/>
-                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/>
+                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
             </output_collection>
         </test>
         <test>
@@ -116,8 +115,8 @@
             <output_collection name="transcripts" type="list">
                 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
                 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/>
                 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
                 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
             </output_collection>
@@ -150,8 +149,16 @@
                 author = {Eric Wafula},
                 title = {None},
                 year = {None},
-                eprint = {None},
-                url = {None}
+		url = {https://github.com/dePamphilis/PlantTribes}
             }</citation>
+            <citation type="bibtex">
+                @published{Proc Int Conf Intell Syst Mol Biol,
+                author = {Iseli C, Jongeneel CV, Bucher P.},
+                title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
+                year = {1999},
+		url = {http://estscan.sourceforge.net/}
+            }</citation>
+            <citation type="doi">10.1038/nprot.2013.084</citation>
+	    <citation type="doi">10.1109/tcbb.2013.68</citation>
     </citations>
 </tool>