opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

adding hapmapmart.xml to tools/data_source

Browse Source
This commit is contained in:
Ross Lazarus
2010-11-18 10:30:27 -05:00
parent 9e6d11bc46
commit d1270499ea
1 changed files with 46 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/data_source/hapmapmart.xml
+46
View File
@@ -0,0 +1,46 @@
<?xml version="1.0"?>
<!--
hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed
the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately
to create reliable pedigrees. eesh...
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.
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
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
-->
<tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01">
<description>HapMap Biomart</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
<display>go to HapMap BioMart $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
</inputs>
<request_param_translation>
<request_param galaxy_name="URL" remote_name="URL" missing="">
<append_param separator="&amp;" first_separator="?" join="=">
<value name="_export" missing="1" />
<value name="GALAXY_URL" missing="0" />
</append_param>
</request_param>
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
<value_translation>
<value galaxy_value="tabular" remote_value="TSV" />
</value_translation>
</request_param>
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" />
<request_param galaxy_name="organism" remote_name="organism" missing="human" />
<request_param galaxy_name="table" remote_name="table" missing="" />
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="HapMap query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
<data name="output" format="tabular" />
</outputs>
<options sanitize="False" refresh="True"/>
</tool>