Fixed genomespace_importer.xml command block

This commit is contained in:
slugger70
2017-08-19 00:38:06 +05:30
committed by Nuwan Goonasekera
parent ad1b613445
commit b04ccbe55b
+4 -2
View File
@@ -1,7 +1,9 @@
<?xml version="1.0"?>
<tool name="GenomeSpace Importer" id="genomespace_importer" require_login="False" version="0.0.4">
<description> - receive data from GenomeSpace</description>
<command interpreter="python">genomespace_importer.py
<command><![CDATA[
export PYTHONPATH=$__root_dir__/lib:\$PYTHONPATH &&
$__root_dir__/.venv/bin/python $__root_dir__/tools/genomespace/genomespace_importer.py
#set $input_file = $URL.split("^")[0] if "^" in $URL else $URL
#set $token = $URL.split("^")[1] if "^" in $URL and $URL.split("^")[1] else $__user__.preferences.get( 'genomespace_token', None )
@@ -10,7 +12,7 @@
--json_parameter_file "${output_file1}"
--galaxy_root $__root_dir__
--data_conf $__datatypes_config__
</command>
]]></command>
<!-- If using this tool through bioblend, the URL parameter should contain the path to the GenomeSpaceFile + the security token
separated by a ^ as follows: GenomeSpaceFilePath^Token -->
<inputs check_values="False">