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Merge pull request #275 from martenson/data-source-fix

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[15.05] fix the data source tools for modendcode with proper URLs
This commit is contained in:
Nate Coraor
2015-05-20 15:15:33 -04:00
parent 9e67ba6de2 8d2f9f77eb
commit 0dc7669646
3 changed files with 11 additions and 11 deletions
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tool-data/shared/gbrowse/gbrowse_build_sites.txt
+1 -1
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@@ -18,7 +18,7 @@ wormbase_ws225 WormBase WS225 http://ws225.wormbase.org/db/gb2/gbrowse/ caeAng1,
tair tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis,Arabidopsis_thaliana_TAIR10 arabidopsis_tair8,arabidopsis_tair9,arabidopsis
#modENCODE
modencode modENCODE http://modencode.oicr.on.ca/fgb2/gbrowse/ ce6,dm2 worm,fly
modencode modENCODE http://gbrowse.modencode.org/fgb2/gbrowse/ ce10,dm3 worm,fly
#Saccharomyces Genome Database (SGD)
sgd_yeast Saccharomyces Genome Database http://browse.yeastgenome.org/fgb2/gbrowse/ Saccharomyces_cerevisiae_S288C_SGD2010 scgenome
tools/data_source/fly_modencode.xml
+5 -5
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@@ -1,21 +1,21 @@
<?xml version="1.0"?>
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.0">
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.1">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/fly" check_values="false" target="_top">
<inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/fly" check_values="false" target="_top">
<display>go to modENCODE fly server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" />
</inputs>
<request_param_translation>
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm2" >
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm3" >
<value_translation>
<value galaxy_value="dm2" remote_value="fly" />
<value galaxy_value="dm3" remote_value="fly" />
</value_translation>
</request_param>
<request_param galaxy_name="URL" remote_name="URL" missing="">
<append_param separator="&amp;" first_separator="?" join="=">
<value name="d" missing="" />
<value name="dbkey" missing="dm2" />
<value name="dbkey" missing="dm3" />
<value name="q" missing="" />
<value name="s" missing="" />
<value name="t" missing="" />
tools/data_source/worm_modencode.xml
+5 -5
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@@ -1,21 +1,21 @@
<?xml version="1.0"?>
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.0">
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.1">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/worm" check_values="false" target="_top">
<inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/worm" check_values="false" target="_top">
<display>go to modENCODE worm server $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" />
</inputs>
<request_param_translation>
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce6" >
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce10" >
<value_translation>
<value galaxy_value="ce6" remote_value="worm" />
<value galaxy_value="ce10" remote_value="worm" />
</value_translation>
</request_param>
<request_param galaxy_name="URL" remote_name="URL" missing="">
<append_param separator="&amp;" first_separator="?" join="=">
<value name="d" missing="" />
<value name="dbkey" missing="ce6" />
<value name="dbkey" missing="ce10" />
<value name="q" missing="" />
<value name="s" missing="" />
<value name="t" missing="" />