[hg] galaxy 1579: Add new EpiGRAPH tools that point to EpiGRAPH ...

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[hg] galaxy 1579: Add new EpiGRAPH tools that point to EpiGRAPH ...

Greg Von Kuster
details:   http://www.bx.psu.edu/hg/galaxy/rev/778fcc385ab7
changeset: 1579:778fcc385ab7
user:      Greg Von Kuster <[hidden email]>
date:      Tue Oct 28 11:27:42 2008 -0400
description:
Add new EpiGRAPH tools that point to EpiGRAPH production server.

6 file(s) affected in this change:

tool_conf.xml.main
tool_conf.xml.sample
tools/data_destination/epigraph.xml
tools/data_destination/epigraph_test.xml
tools/data_source/epigraph_import.xml
tools/data_source/epigraph_import_test.xml

diffs (144 lines):

diff -r 75312c1cab05 -r 778fcc385ab7 tool_conf.xml.main
--- a/tool_conf.xml.main Tue Oct 28 10:55:39 2008 -0400
+++ b/tool_conf.xml.main Tue Oct 28 11:27:42 2008 -0400
@@ -7,6 +7,7 @@
     <tool file="data_source/microbial_import.xml" />
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/encode_db.xml" />
+    <tool file="data_source/epigraph_import.xml" />
   </section>
   <section name="Get ENCODE Data" id="encode">
     <tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/>
@@ -15,6 +16,9 @@
     <tool file="data_source/encode_import_transcription_regulation.xml"/>
     <tool file="data_source/encode_import_all_latest_datasets.xml" />
     <tool file="data_source/encode_import_gencode.xml" />
+  </section>
+  <section name="Send Data" id="send">
+    <tool file="data_destination/epigraph.xml" />
   </section>
   <section name="ENCODE Tools" id="EncodeTools">
     <tool file="encode/gencode_partition.xml" />
diff -r 75312c1cab05 -r 778fcc385ab7 tool_conf.xml.sample
--- a/tool_conf.xml.sample Tue Oct 28 10:55:39 2008 -0400
+++ b/tool_conf.xml.sample Tue Oct 28 11:27:42 2008 -0400
@@ -11,8 +11,9 @@
     <tool file="data_source/biomart_test.xml" />
     <tool file="data_source/gbrowse_elegans.xml" />
     <tool file="data_source/flymine.xml" />
+    <tool file="data_source/encode_db.xml" />
     <tool file="data_source/epigraph_import.xml" />
-    <tool file="data_source/encode_db.xml" />
+    <tool file="data_source/epigraph_import_test.xml" />
     <tool file="data_source/hbvar.xml" />
     <tool file="validation/fix_errors.xml" />
   </section>
@@ -26,6 +27,7 @@
   </section>
   <section name="Send Data" id="send">
     <tool file="data_destination/epigraph.xml" />
+    <tool file="data_destination/epigraph_test.xml" />
   </section>
   <section name="ENCODE Tools" id="EncodeTools">
     <tool file="encode/gencode_partition.xml" />
diff -r 75312c1cab05 -r 778fcc385ab7 tools/data_destination/epigraph.xml
--- a/tools/data_destination/epigraph.xml Tue Oct 28 10:55:39 2008 -0400
+++ b/tools/data_destination/epigraph.xml Tue Oct 28 11:27:42 2008 -0400
@@ -6,7 +6,7 @@
         <param format="bed" name="input1" type="data" label="Send this dataset to EpiGRAPH">
             <validator type="unspecified_build" />
         </param>
-        <param name="REDIRECT_URL" type="hidden" value="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/DataImport.jsp" />
+        <param name="REDIRECT_URL" type="hidden" value="http://epigraph.mpi-inf.mpg.de/WebGRAPH/faces/DataImport.jsp" />
         <param name="DATA_URL" type="baseurl" value="/datasets" />
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" />
     </inputs>
diff -r 75312c1cab05 -r 778fcc385ab7 tools/data_destination/epigraph_test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/data_destination/epigraph_test.xml Tue Oct 28 11:27:42 2008 -0400
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<tool name="Perform genome analysis" id="epigraph_test_export">
+    <description> and prediction with EpiGRAPH Test</description>
+    <redirect_url_params>GENOME=${input1.dbkey} NAME=${input1.name} INFO=${input1.info}</redirect_url_params>
+    <inputs>
+        <param format="bed" name="input1" type="data" label="Send this dataset to EpiGRAPH">
+            <validator type="unspecified_build" />
+        </param>
+        <param name="REDIRECT_URL" type="hidden" value="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/DataImport.jsp" />
+        <param name="DATA_URL" type="baseurl" value="/datasets" />
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" />
+    </inputs>
+    <outputs/>
+    <help>
+
+.. class:: warningmark
+
+After clicking the **Execute** button, you will be redirected to the EpiGRAPH test website. Please be patient while the dataset is being imported. Inside EpiGRAPH, buttons are available to send the results of the EpiGRAPH analysis back to Galaxy. In addition, you can always abandon an EpiGRAPH session and return to Galaxy by directing your browser to your current Galaxy instance.
+
+-----
+
+.. class:: infomark
+
+**What it does**
+
+This tool sends the selected dataset to EpiGRAPH in order to perform an in-depth analysis with statistical and machine learning methods.
+
+-----
+
+.. class:: infomark
+
+**EpiGRAPH outline**
+
+The EpiGRAPH_ web service enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload or import sets of genomic regions and EpiGRAPH will test a wide range of attributes (including DNA sequence and structure, gene density, chromatin modifications and evolutionary conservation) for enrichment or depletion among these regions. Furthermore, EpiGRAPH learns to predictively identify genomic regions that exhibit similar properties.
+
+.. _EpiGRAPH: http://epigraph.mpi-inf.mpg.de/
+
+    </help>
+</tool>
+
diff -r 75312c1cab05 -r 778fcc385ab7 tools/data_source/epigraph_import.xml
--- a/tools/data_source/epigraph_import.xml Tue Oct 28 10:55:39 2008 -0400
+++ b/tools/data_source/epigraph_import.xml Tue Oct 28 11:27:42 2008 -0400
@@ -7,7 +7,7 @@
 <tool name="EpiGRAPH" id="epigraph_import" tool_type="data_source" URL_method="get">
     <description> server</description>
     <command interpreter="python">data_source.py $output</command>
-    <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/Login.jsp" check_values="false" method="get">
+    <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH/faces/Login.jsp" check_values="false" method="get">
         <display>go to EpiGRAPH server $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import" />
     </inputs>
diff -r 75312c1cab05 -r 778fcc385ab7 tools/data_source/epigraph_import_test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/data_source/epigraph_import_test.xml Tue Oct 28 11:27:42 2008 -0400
@@ -0,0 +1,29 @@
+<?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="EpiGRAPH" id="epigraph_import_test" tool_type="data_source" URL_method="get">
+    <description> test server</description>
+    <command interpreter="python">data_source.py $output</command>
+    <inputs action="http://epigraph.mpi-inf.mpg.de/WebGRAPH_Public_Test/faces/Login.jsp" check_values="false" method="get">
+        <display>go to EpiGRAPH server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=epigraph_import_test" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="dbkey" remote_name="GENOME" 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="EpiGRAPH 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>