[galaxy-commits] commit/galaxy-central: dan: Add EBI ENA SRA tool contributed by Iain Cleland.

[Bitbucket]

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/d00337a396ff/
changeset:   d00337a396ff
user:        dan
date:        2011-12-13 15:45:49
summary:     Add EBI ENA SRA tool contributed by Iain Cleland.
affected #:  3 files

diff -r 7dd3a089101138a4796eb73a5f1391d2f436723e -r d00337a396ffd79e78ed38b9365e66d055b1cfc4 tool_conf.xml.main
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -5,6 +5,7 @@
     <tool file="data_source/ucsc_tablebrowser.xml" /><tool file="data_source/ucsc_tablebrowser_archaea.xml" /><tool file="data_source/bx_browser.xml" />
+    <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" />


diff -r 7dd3a089101138a4796eb73a5f1391d2f436723e -r d00337a396ffd79e78ed38b9365e66d055b1cfc4 tool_conf.xml.sample
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -6,6 +6,7 @@
     <tool file="data_source/ucsc_tablebrowser_test.xml" /><tool file="data_source/ucsc_tablebrowser_archaea.xml" /><tool file="data_source/bx_browser.xml" />
+    <tool file="data_source/ebi_sra.xml"/><tool file="data_source/microbial_import.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/biomart_test.xml" />


diff -r 7dd3a089101138a4796eb73a5f1391d2f436723e -r d00337a396ffd79e78ed38b9365e66d055b1cfc4 tools/data_source/ebi_sra.xml
--- /dev/null
+++ b/tools/data_source/ebi_sra.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool name="EBI SRA" id="ebi_sra_main" tool_type="data_source" version="1.0.0">
+    <description>ENA SRA</description>
+    <!-- This paython script imports the file into Galaxy -->
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <!-- The URL where Galaxy will forwars the user when this tool is accessed from the Get Data menu -->
+    <inputs action="http://www.ebi.ac.uk/ena/" check_values="false" method="get"> 
+        <display>go to EBI SRA server $GALAXY_URL</display>
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="fastq"/>
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>

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

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