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https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
f92b25d2f5
Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles. Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes. Future Enhancement: Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
43 lines
2.5 KiB
XML
43 lines
2.5 KiB
XML
<?xml version="1.0"?>
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<!--
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If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
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the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
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initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
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TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
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everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
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-->
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<tool name="GrameneMart" id="gramenemart" tool_type="data_source" version="1.0.1">
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<description> Central server</description>
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<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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<inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top">
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<display>go to GrameneMart Central $GALAXY_URL</display>
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<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
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</inputs>
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<request_param_translation>
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<request_param galaxy_name="URL" remote_name="URL" missing="">
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<append_param separator="&" first_separator="?" join="=">
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<value name="_export" missing="1" />
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<value name="GALAXY_URL" missing="0" />
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</append_param>
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</request_param>
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<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular">
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<value_translation>
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<value galaxy_value="tabular" remote_value="TSV" />
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</value_translation>
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</request_param>
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<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
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<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
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<request_param galaxy_name="organism" remote_name="organism" missing="" />
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<request_param galaxy_name="table" remote_name="table" missing="" />
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<request_param galaxy_name="description" remote_name="description" missing="" />
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<request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
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<request_param galaxy_name="info" remote_name="info" missing="" />
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</request_param_translation>
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<uihints minwidth="800"/>
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<outputs>
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<data name="output" format="tabular" />
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</outputs>
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<options sanitize="False" refresh="True"/>
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</tool>
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