Mercurial > repos > matnguyen > pathogist

changeset 8:7708da43aefb draft

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Add run_all
author matnguyen
date Mon, 11 Mar 2019 03:27:37 -0400
parents 4bfb3a8dd955
children 728c6b81b45e
files galaxy/tools/config_builder/config_builder.xml galaxy/tools/run_all/run_all.xml
diffstat 2 files changed, 28 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>
 
 
--- /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>