Mercurial > repos > cropgeeks > flapjack

changeset 6:e8083821455b draft

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Uploaded
author cropgeeks
date Tue, 21 Feb 2017 08:34:36 -0500
parents 735f690bdb76
children 1471a0665007
files createproject.xml datatypes_conf.xml flapjack.py
diffstat 3 files changed, 9 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/createproject.xml	Tue Feb 21 08:18:53 2017 -0500
+++ b/createproject.xml	Tue Feb 21 08:34:36 2017 -0500
@@ -12,7 +12,9 @@
   <description>Run pedigree verification of F1s (known parents) analysis</description>
   <command><![CDATA[
   java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject 
-  -map=$map -genotypes=$genotypes -galaxyHTML=$html -project=$output
+  -map=$map -genotypes=$genotypes
+##  -galaxyHTML=$html 
+  -project=$output
   ]]>
   </command>
   <inputs>
@@ -35,7 +37,7 @@
   <outputs>
   <!-- label="${tool.name} on ${on_string}: project.flapjack" -->
     <data name="output" format="flapjack" />
-	<data name="html" format="html" />
+	<!--<data name="html" format="html" />-->
   </outputs>
   
   <stdio>
--- a/datatypes_conf.xml	Tue Feb 21 08:18:53 2017 -0500
+++ b/datatypes_conf.xml	Tue Feb 21 08:34:36 2017 -0500
@@ -14,7 +14,8 @@
        <datatype extension="fjgraph" type="galaxy.datatypes.flapjack:FlapjackGraphFormat" mimetype="text/plain" display_in_upload="true"/>
     </registration>
     <sniffers>
-       <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackProjectFormat"/>
+	   <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/>
        <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/>
        <sniffer type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat"/>
        <sniffer type="galaxy.datatypes.flapjack:FlapjackQtlFormat"/>
--- a/flapjack.py	Tue Feb 21 08:18:53 2017 -0500
+++ b/flapjack.py	Tue Feb 21 08:34:36 2017 -0500
@@ -1,5 +1,8 @@
 from galaxy.datatypes.data import Text
 
+class FlapjackProjectFormat(Text):
+    file_ext = "flapjack"
+
 class FlapjackMapFormat(Text):
     file_ext = "fjmap"