# HG changeset patch
# User iuc
# Date 1488192130 18000
# Node ID f40b6a8c60f239b6bdea45b86b30f9e4694890b6
# Parent  6fb6281a836fbc4e53db2da483a8cd0e525a2b1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 9401451df4a985ef5686864eaadafa077ffc0877

diff -r 6fb6281a836f -r f40b6a8c60f2 macros.xml
--- a/macros.xml	Mon Sep 26 11:42:57 2016 -0400
+++ b/macros.xml	Mon Feb 27 05:42:10 2017 -0500
@@ -38,9 +38,9 @@
 
 **Project links:**
 
-`Stacks website <http://creskolab.uoregon.edu/stacks/>`_
+`Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_
 
-`Stacks manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_
+`Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_
 
 `Stacks google group <http://groups.google.com/group/stacks-users>`_
 ]]></token>
diff -r 6fb6281a836f -r f40b6a8c60f2 stacks_refmap.xml
--- a/stacks_refmap.xml	Mon Sep 26 11:42:57 2016 -0400
+++ b/stacks_refmap.xml	Mon Feb 27 05:42:10 2017 -0500
@@ -11,7 +11,7 @@
 
         #if str( $options_usage.rad_analysis_type ) == "genetic":
             #for $input_parent in $options_usage.parent_alignments:
-                #if $input_parent.ext == "sam":
+                #if $input_parent.is_of_type('sam'):
                     #set $data_path = splitext($input_parent.element_identifier)[0]
                     #set $data_path = re.sub(r'\.1$', '', $data_path)
                     #set $data_path = $data_path + ".sam"
@@ -27,7 +27,7 @@
             #for $input_progeny in $options_usage.progeny_alignments:
 
                 #if $input_progeny:
-                    #if $input_progeny.ext == "sam":
+                    #if $input_progeny.is_of_type('sam'):
                         #set $data_path = splitext($input_progeny.element_identifier)[0]
                         #set $data_path = re.sub(r'\.1$', '', $data_path)
                         #set $data_path = $data_path + ".sam"
@@ -43,7 +43,7 @@
         #else:
             #for $input_indiv in $options_usage.individual_sample:
 
-                #if $input_indiv.ext == "sam":
+                #if $input_indiv.is_of_type('sam'):
                     #set $data_path = splitext($input_indiv.element_identifier)[0]
                     #set $data_path = re.sub(r'\.1$', '', $data_path)
                     #set $data_path = $data_path + ".sam"
@@ -67,7 +67,7 @@
 
             #if str( $options_usage.rad_analysis_type ) == "genetic":
                 #for $input_parent in $options_usage.parent_alignments:
-                    #if $input_parent.ext == "sam":
+                    #if $input_parent.is_of_type('sam'):
                         #set $data_path = splitext($input_parent.element_identifier)[0]
                         #set $data_path = re.sub(r'\.1$', '', $data_path)
                         #set $data_path = $data_path + ".sam"
@@ -84,7 +84,7 @@
 
                 #for $input_progeny in $options_usage.progeny_alignments:
                     #if $input_progeny:
-                        #if $input_progeny.ext == "sam":
+                        #if $input_progeny.is_of_type('sam'):
                             #set $data_path = splitext($input_progeny.element_identifier)[0]
                             #set $data_path = re.sub(r'\.1$', '', $data_path)
                             #set $data_path = $data_path + ".sam"
@@ -100,7 +100,7 @@
             #else:
                 #for $input_indiv in $options_usage.individual_sample:
 
-                    #if $input_indiv.ext == "sam":
+                    #if $input_indiv.is_of_type('sam'):
                         #set $data_path = splitext($input_indiv.element_identifier)[0]
                         #set $data_path = re.sub(r'\.1$', '', $data_path)
                         #set $data_path = $data_path + ".sam"