Mercurial > repos > melissacline > ucsc_xena_platform
changeset 18:154a9b440b63
Updated the xena jar to version 14, updated the URL of the Xena pages
| author | melissacline |
|---|---|
| date | Tue, 02 Jun 2015 14:55:55 -0700 |
| parents | 6785e729c7ad (diff) c298bb05640e (current diff) |
| children | 782e91e9ef48 |
| files | ucsc_xena_datapages.xml ucsc_xena_hub.xml ucsc_xenabrowser.xml xena.jar xena_utils.pyc |
| diffstat | 5 files changed, 7 insertions(+), 8 deletions(-) [+] |
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--- a/ucsc_xena_datapages.xml Thu Apr 23 08:45:54 2015 -0700 +++ b/ucsc_xena_datapages.xml Tue Jun 02 14:55:55 2015 -0700 @@ -4,13 +4,13 @@ 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="Explore Data in Xena" id="ucsc_xena_datapages" tool_type="data_source"> +<tool name="Explore Data in Xena" id="ucsc_xenadatapages" tool_type="data_source"> <description>Browse the UCSC Xena Data Pages.</description> - <command interpreter="python">ucsc_xena_download.py $genomic $clinical $__app__.config.output_size_limit</command> - <inputs action="https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/" check_values="false" method="get"> - <display>go to UCSC Xena Data $GALAXY_URL</display> + <command interpreter="python">ucsc_xena_download.py $genomic $__app__.config.output_size_limit</command> + <inputs action="https://genome-cancer.ucsc.edu/proj/site/xena/datapages/" check_values="false" method="get"> + <display>Explore the data in Xena $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> - <param name="tool_id" type="hidden" value="ucsc_xena_datapages" /> + <param name="tool_id" type="hidden" value="ucsc_xenadatapages" /> </inputs> <request_param_translation> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> @@ -19,7 +19,6 @@ <uihints minwidth="800"/> <outputs> <data name="genomic" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' genomic'" /> - <data name="clinical" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' clinical'"/> </outputs> <options sanitize="False" refresh="True"/> </tool>
--- a/ucsc_xena_hub.xml Thu Apr 23 08:45:54 2015 -0700 +++ b/ucsc_xena_hub.xml Tue Jun 02 14:55:55 2015 -0700 @@ -7,7 +7,7 @@ <tool name="Xena Data Hub" id="ucsc_xenadatahub" tool_type="data_source"> <description>Select your Xena Data Hub</description> <command interpreter="python">ucsc_xena_download.py $genomic $__app__.config.output_size_limit</command> - <inputs action="https://genome-cancer.soe.ucsc.edu/proj/site/xena/hub/" check_values="false" method="get"> + <inputs action="https://genome-cancer.ucsc.edu/proj/site/xena/hub/" check_values="false" method="get"> <display>Select your Xena Data Hub $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> <param name="tool_id" type="hidden" value="ucsc_xenadatapages" />
--- a/ucsc_xenabrowser.xml Thu Apr 23 08:45:54 2015 -0700 +++ b/ucsc_xenabrowser.xml Tue Jun 02 14:55:55 2015 -0700 @@ -7,7 +7,7 @@ <tool name="UCSC Xena Browser" id="ucsc_xenabrowser" tool_type="data_source"> <description>Run the UCSC Xena Browser as a Galaxy tool.</description> <command interpreter="python">ucsc_xena_download.py $genomic $clinical $__app__.config.output_size_limit</command> - <inputs action="https://genome-cancer.soe.ucsc.edu/proj/site/xena/heatmap" check_values="false" method="get"> + <inputs action="https://genome-cancer.ucsc.edu/proj/site/xena/heatmap/" check_values="false" method="get"> <display>go to UCSC Xena Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> <param name="tool_id" type="hidden" value="ucsc_xenabrowser" />