Mercurial > repos > mvdbeek > symlink_files

changeset 2:301f0997a1da draft default tip

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planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
author mvdbeek
date Tue, 29 Nov 2016 10:53:10 -0500
parents 46dc0dbd9f04
children
files symlink_files.xml
diffstat 1 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/symlink_files.xml	Tue Nov 29 10:14:01 2016 -0500
+++ b/symlink_files.xml	Tue Nov 29 10:53:10 2016 -0500
@@ -15,9 +15,9 @@
                 #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'
+               ln -fs \$(readlink '$input') '$output_path'/'$input.element_identifier'.'$input.ext'
             #else:
-               ln -fs '$input' '$output_path'/'$input.element_identifier'
+               ln -fs \$(readlink '$input') '$output_path'/'$input.element_identifier'
             #end if
         #end if
         #if $input_collection:
@@ -26,21 +26,21 @@
                 #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'.'$element.ext';
+                    ln -fs \$(readlink '$element') '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext';
             #end for
         #end if
         #if $input_collection_paired:
             mkdir -p '$output_path'/'$input_collection_paired.name' &&
             #for $element in $input_collection_paired:
-                ln -fs '$element.forward' '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-forward.'$element.ext';
-                ln -fs '$element.reverse' '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-reverse.'$element.ext';
+                ln -fs \$(readlink '$element.forward') '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-forward.'$element.ext';
+                ln -fs \$(readlink '$element.reverse') '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-reverse.'$element.ext';
             #end for
         #end if
         #if $input_collection_list_paired:
             #for $sample in $input_collection_list_paired:
             mkdir -p '$output_path'/'$input_collection_list_paired.name' &&
                 #for $element in $sample:
-                    ln -fs '$element' '$output_path'/'$input_collection_list_paired.name'/'$sample.name'-$element.element_identifier.'$element.ext';
+                    ln -fs \$(readlink '$element') '$output_path'/'$input_collection_list_paired.name'/'$sample.name'-$element.element_identifier.'$element.ext';
                 #end for
             #end for
         #end if