1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/2577b386dbbe/ Changeset: 2577b386dbbe User: dan Date: 2014-06-27 20:44:55 Summary: Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0. Affected #: 9 files

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -7,7 +7,12 @@ <tool file="data_source/ebi_sra.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/gramene_mart.xml" /> + <tool file="data_source/flymine.xml" /><tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /> + <tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" />

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -12,6 +12,13 @@ <tool file="data_source/cbi_rice_mart.xml" /><tool file="data_source/gramene_mart.xml" /><tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/flymine.xml" /> + <tool file="data_source/flymine_test.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/mousemine.xml" /> + <tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /> + <tool file="data_source/metabolicmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/wormbase_test.xml" />

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/flymine.xml --- /dev/null +++ b/tools/data_source/flymine.xml @@ -0,0 +1,35 @@ +<?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="Flymine" id="flymine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.flymine.org" check_values="false" method="get"> + <display>go to Flymine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <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="FlyMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect --> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> +

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/flymine_test.xml --- /dev/null +++ b/tools/data_source/flymine_test.xml @@ -0,0 +1,31 @@ +<?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="Flymine test" id="flymine_test" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get"> + <display>go to Flymine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <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="FlyMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> +

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/metabolicmine.xml --- /dev/null +++ b/tools/data_source/metabolicmine.xml @@ -0,0 +1,13 @@ +<?xml version="1.0"?> +<tool name="metabolicMine" id="metabolicmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get"> + <display>go to metabolicMine server $GALAXY_URL</display> + </inputs> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/modmine.xml --- /dev/null +++ b/tools/data_source/modmine.xml @@ -0,0 +1,19 @@ +<?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="modENCODE modMine" id="modmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://intermine.modencode.org/" check_values="false" method="get"> + <display>go to modENCODE modMine server $GALAXY_URL</display> + </inputs> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> +

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/mousemine.xml --- /dev/null +++ b/tools/data_source/mousemine.xml @@ -0,0 +1,35 @@ +<?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="MouseMine" id="mousemine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get"> + <display>go to MouseMine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=mousemine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <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="MouseMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect --> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> +

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/ratmine.xml --- /dev/null +++ b/tools/data_source/ratmine.xml @@ -0,0 +1,34 @@ +<?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="Ratmine" id="ratmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get"> + <display>go to Ratmine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <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="Ratmine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect --> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

diff -r 60be24933d59806e355d64a5156327021027772d -r 2577b386dbbe421e80c816abf7683359ab64fe1f tools/data_source/yeastmine.xml --- /dev/null +++ b/tools/data_source/yeastmine.xml @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<tool name="YeastMine" id="yeastmine" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get"> + <display>go to yeastMine server $GALAXY_URL</display> + </inputs> + <request_param_translation> + <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" > + <value_translation> + <value galaxy_value="auto" remote_value="txt" /><!-- intermine currently always provides 'txt', make this auto detect --> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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