Mercurial > repos > mvdbeek > symlink_files

changeset 1:46dc0dbd9f04 draft

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planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
author mvdbeek
date Tue, 29 Nov 2016 10:14:01 -0500
parents 909a7e8e9b30
children 301f0997a1da
files symlink_files.xml
diffstat 1 files changed, 7 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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: