Mercurial > repos > mvdbeek > igv_take_screenshots

changeset 26:6f98222928ee draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0437e9e56f0af2ccfb5f119b0f290109807ed9b0-dirty
author mvdbeek
date Fri, 15 Jun 2018 13:01:15 -0400
parents c96924da37af
children 676591c44f64
files igv_make_screenshots.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/igv_make_screenshots.xml	Fri Jun 15 12:56:58 2018 -0400
+++ b/igv_make_screenshots.xml	Fri Jun 15 13:01:15 2018 -0400
@@ -4,9 +4,10 @@
 #set $dataset_id = str($__app__.security.encode_id($inputsection.input.dataset.id))
 #set $user_id = str($__app__.security.encode_id($__user_id__))
 #set $galaxy_url = $__app__.config.galaxy_infrastructure_url
-#set $ext = $inputsection.input.extension
+#set $file_ext = $inputsection.input.extension
+#set $igv_ext = $ext if $file_ext != "gff3" else "gff"
 #set $element_identifier = $inputsection.input.element_identifier
-#set $display_link = "{galaxy_url}/display_application/{dataset_id}/igv_{ext}/local_default/None/data/galaxy_{dataset_id}.{ext}".format(galaxy_url=galaxy_url, dataset_id=dataset_id, ext=ext, user_id=user_id)
+#set $display_link = "{galaxy_url}/display_application/{dataset_id}/igv_{ext}/local_default/None/data/galaxy_{dataset_id}.{file_ext}".format(galaxy_url=galaxy_url, dataset_id=dataset_id, igv_ext=igv_ext, file_ext=file_ext, user_id=user_id)
 ]]></token>
         <token name="@PATH@"><![CDATA[#set $path="%s.%s.%s" % ($i, $inputsection.input.element_identifier, $inputsection.input.extension)]]></token>
     </macros>