# HG changeset patch
# User greg
# Date 1485887689 18000
# Node ID db0c2baf176fac37c8be747de641c587d8fed1f6
# Parent  5a0a049d11aa693f5bc7eec7f8e5a7105f85afeb
Uploaded

diff -r 5a0a049d11aa -r db0c2baf176f assembly_post_processor.xml
--- a/assembly_post_processor.xml	Tue Jan 31 11:23:32 2017 -0500
+++ b/assembly_post_processor.xml	Tue Jan 31 13:34:49 2017 -0500
@@ -13,6 +13,7 @@
     </stdio>
     <command>
         <![CDATA[
+            #import os
             AssemblyPostProcesser
             --transcripts '$input'
             --prediction_method $prediction_method_cond.prediction_method
@@ -21,9 +22,12 @@
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
+                    #set scaffold_path = '$options_type.target_gene_family_assembly_cond.scaffold.path'
+                    #set scaffold_dir = os.path.split($scaffold_path)[0]
+                    #set scaffold = os.path.split($scaffold_path)[1]
                     --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
-                    --scaffold_dir '$options_type.target_gene_family_assembly_cond.scaffold.path'
-                    --scaffold '$options_type.target_gene_family_assembly_cond.scaffold'
+                    --scaffold_dir $scaffold_dir
+                    --scaffold $scaffold
                     --method '$options_type.target_gene_family_assembly_cond.method'
                 #end if
                 --gap_trimming $options_type.gap_trimming
@@ -67,7 +71,7 @@
                         <param name="orthogroups" format="tabular" type="data" label="List of orthogroup identifiers for target gene families to assemble"/>
                         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
                             <options from_data_table="plant_tribes_scaffolds" />
-                            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
+                            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
                         </param>
                         <param name="method" type="select" label="Protein clustering method">
                             <option value="gfam" selected="true">GFam</option>
@@ -149,16 +153,16 @@
                 author = {Eric Wafula},
                 title = {None},
                 year = {None},
-		url = {https://github.com/dePamphilis/PlantTribes}
+                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/}
+                url = {http://estscan.sourceforge.net/}
             }</citation>
             <citation type="doi">10.1038/nprot.2013.084</citation>
-	    <citation type="doi">10.1109/tcbb.2013.68</citation>
+            <citation type="doi">10.1109/tcbb.2013.68</citation>
     </citations>
 </tool>