# HG changeset patch
# User mvdbeek
# Date 1480432441 18000
# Node ID 46dc0dbd9f04a8a242b3914c9cfbbc9f7eb5a8fd
# Parent  909a7e8e9b304bf60bc6fbd7599b02f09f3fe539
planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba

diff -r 909a7e8e9b30 -r 46dc0dbd9f04 symlink_files.xml
--- a/symlink_files.xml	Tue Nov 29 10:03:30 2016 -0500
+++ b/symlink_files.xml	Tue Nov 29 10:14:01 2016 -0500
@@ -12,6 +12,9 @@
         #if $input:
             mkdir -p '$output_path' &&
             #if '$input.ext':
+                #if input.ext == 'bam':
+                    ln -fs '$input.metadata.bam_index' '$output_path'/'$input.element_identifier'.'$input.ext'.bai &&
+                #end if
                ln -fs '$input' '$output_path'/'$input.element_identifier'.'$input.ext'
             #else:
                ln -fs '$input' '$output_path'/'$input.element_identifier'
@@ -20,7 +23,10 @@
         #if $input_collection:
             mkdir -p '$output_path'/'$input_collection.name' &&
             #for $element in $input_collection:
-                ln -fs '$element' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext';
+                #if $element.ext == 'bam':
+                    ln -fs '$element.metadata.bam_index' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext'.bai &&
+                #end if
+                    ln -fs '$element' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext';
             #end for
         #end if
         #if $input_collection_paired: