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Update GenomeSpace tools to use __user__ as needed.

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Daniel Blankenberg
2013-05-03 16:02:40 -04:00
parent 9fb2031b04
commit 14cec88abc
2 changed files with 7 additions and 9 deletions
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tools/genomespace/genomespace_exporter.xml
+4 -5
View File
@@ -3,10 +3,9 @@
<description> - send data to GenomeSpace</description>
<command interpreter="python">genomespace_exporter.py
--genomespace_site "prod"
#assert $__user_id__ != 'Anonymous', Exception( 'You must be logged in to use this tool.' )
#set $user = $__app__.model.User.get( $__user_id__ )
#set $username = $user.preferences.get( 'genomespace_username', None )
#set $token = $user.preferences.get( 'genomespace_token', None )
#assert $__user__, Exception( 'You must be logged in to use this tool.' )
#set $username = $__user__.preferences.get( 'genomespace_username', None )
#set $token = $__user__.preferences.get( 'genomespace_token', None )
#assert None not in ( $username, $token ), Exception( 'You must associate a GenomeSpace OpenID with your account and log in with it.' )
#import binascii
--username "${username}"
@@ -36,7 +35,7 @@
<inputs>
<param format="data" name="input1" type="data" label="Send this dataset to GenomeSpace" />
<param name="base_url" type="baseurl" />
<param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1 )" help="Leave blank to generate automatically"/>
<param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1 )" help="Leave blank to generate automatically"/>
<param name="filename" type="text" size="80" help="Leave blank to generate automatically" />
</inputs>
<outputs>
tools/genomespace/genomespace_importer.xml
+3 -4
View File
@@ -3,10 +3,9 @@
<description> - receive data from GenomeSpace</description>
<command interpreter="python">genomespace_importer.py
--genomespace_site "prod"
#assert $__user_id__ != 'Anonymous', Exception( 'You must be logged in to use this tool.' )
#set $user = $__app__.model.User.get( $__user_id__ )
#set $username = $user.preferences.get( 'genomespace_username', None )
#set $token = $user.preferences.get( 'genomespace_token', None )
#assert $__user__, Exception( 'You must be logged in to use this tool.' )
#set $username = $__user__.preferences.get( 'genomespace_username', None )
#set $token = $__user__.preferences.get( 'genomespace_token', None )
#assert None not in ( $username, $token ), Exception( 'You must associate a GenomeSpace OpenID with your account and log in with it.' )
--username "${username}"
--token "${token}"