# HG changeset patch
# User matnguyen
# Date 1552289257 14400
# Node ID 7708da43aefb255d651d337ba3ecf6081f491426
# Parent  4bfb3a8dd9559108ce5ab8a9b292616d8c164109
Add run_all

diff -r 4bfb3a8dd955 -r 7708da43aefb galaxy/tools/config_builder/config_builder.xml
--- a/galaxy/tools/config_builder/config_builder.xml	Sun Mar 10 00:07:09 2019 -0500
+++ b/galaxy/tools/config_builder/config_builder.xml	Mon Mar 11 03:27:37 2019 -0400
@@ -88,7 +88,7 @@
 
         $forward
         $reverse
-        config.yaml
+        cc
     ]]></command>
 
 
diff -r 4bfb3a8dd955 -r 7708da43aefb galaxy/tools/run_all/run_all.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy/tools/run_all/run_all.xml	Mon Mar 11 03:27:37 2019 -0400
@@ -0,0 +1,27 @@
+<tool id="run_all" name="PathOGiST - Run All" version="1.0.0">
+    <description>: Runs the entire PathOGiST pipeline</description>
+    <requirements>
+        <requirement type="package" version="0.3">pathogist</requirement>
+    </requirements>
+
+    <command><![CDATA[
+        PATHOGIST $config
+    ]]></command>
+
+    <inputs>
+        <param name="config" type="data" format="yaml" label="Config YAML"
+               help="Config YAML file for PathOGiST"/>
+    </inputs>
+
+    <outputs>
+        <data name="clustering" label="Consensus clustering on ${on_string}" format="tabular" from_work_dir="cc.tsv"/>
+    </outputs>
+
+    <help>
+
+    </help>
+
+    <citations>
+
+    </citations>
+</tool>