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