# HG changeset patch
# User greg
# Date 1488467031 18000
# Node ID a39def7197cfdde2371b7146060aa6bf807efe71
# Parent  fa95f44f2e1a17523dbccc30f382cf61ef40b74a
Uploaded

diff -r fa95f44f2e1a -r a39def7197cf assembly_post_processor.xml
--- a/assembly_post_processor.xml	Mon Feb 13 08:09:37 2017 -0500
+++ b/assembly_post_processor.xml	Thu Mar 02 10:03:51 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.4">
+<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.4.0">
     <description>into putative coding sequences</description>
     <requirements>
         <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
@@ -22,6 +22,7 @@
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
+                    --config_dir '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
                     --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
                     --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
                     --method '$options_type.target_gene_family_assembly_cond.method'
@@ -144,21 +145,35 @@
  
     </help>
     <citations>
-            <citation type="bibtex">
-                @unpublished{None,
-                author = {Eric Wafula},
-                title = {None},
-                year = {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>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Eric Wafula},
+            title = {None},
+            year = {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>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {None},
+            title = {HMMER 3.1+ hmmscan search sequence(s) against a profile database},
+            year = {2013},
+            url = {http://hmmer.org/}
+        }</citation>
+        <citation type="bibtex">
+            @published{Genome Research,
+            author = {Huang X, Madan A},
+            title = {CAP3: A DNA sequence assembly program},
+            year = {1999},
+            url = {http://seq.cs.iastate.edu/cap3.html}
+        }</citation>
     </citations>
 </tool>