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Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. #19689

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Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. #19689

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155b198
Data-source tool for DICED databased added, DICED_Datasetbrowser.xml
jaidevjoshi83 Feb 24, 2025
9fe917d
tool_conf.xml.sample updated with new data source tool DICED_Dataset…
jaidevjoshi83 Feb 26, 2025
20ac054
renamed the data source tool file
jaidevjoshi83 Feb 27, 2025
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1 change: 1 addition & 0 deletions lib/galaxy/config/sample/tool_conf.xml.sample
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
<section id="getext" name="Get Data">
<tool file="data_source/diced.xml" />
<tool file="data_source/upload.xml" />
<tool file="data_source/ucsc_tablebrowser.xml" />
<!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
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30 changes: 30 additions & 0 deletions tools/data_source/diced.xml
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@@ -0,0 +1,30 @@
<?xml version="1.0"?>
<!--
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="DICED Database" id="DICED_table_direct1" tool_type="data_source" version="1.0.0">
<description>DICED is a web interface for access to proteolytic peptides</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="https://diced.lerner.ccf.org" check_values="false" method="post">
<display>go to DICED database $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
<param name="tool_id" type="hidden" value="DICED_table_direct1" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
<request_param galaxy_name="URL" remote_name="URL" missing="" />
<request_param galaxy_name="acc" remote_name="acc" missing="" />
<request_param galaxy_name="type" remote_name="type" missing="" />
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />

</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" label="${tool.name}"/>
</outputs>
</tool>

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