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changeset 5:6ab82d8ca805 draft

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Uploaded
author iuc
date Mon, 25 Aug 2014 04:21:34 -0400
parents ca4449689d61
children 5e0f81024cd4
files gemini_interactions.xml gemini_load.xml gemini_macros.xml gemini_pathways.xml
diffstat 4 files changed, 7 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/gemini_interactions.xml	Mon Aug 25 03:19:30 2014 -0400
+++ b/gemini_interactions.xml	Mon Aug 25 04:21:34 2014 -0400
@@ -9,7 +9,7 @@
     <command>
 <![CDATA[
         gemini 
-            --annotation-dir ${annotation_databases}
+            --annotation-dir ${annotation_databases.fields.path}
             #if $gene.gene_selector == 'lof':
                 ## lof interactions is a separate program
                 lof_interactions
--- a/gemini_load.xml	Mon Aug 25 03:19:30 2014 -0400
+++ b/gemini_load.xml	Mon Aug 25 04:21:34 2014 -0400
@@ -9,7 +9,7 @@
     <command>
 <![CDATA[
         gemini 
-            --annotation-dir ${annotation_databases}
+            --annotation-dir ${annotation_databases.fields.path}
             @BINARY@
             -v "${ infile }"
             -t $annotation_type
--- a/gemini_macros.xml	Mon Aug 25 03:19:30 2014 -0400
+++ b/gemini_macros.xml	Mon Aug 25 04:21:34 2014 -0400
@@ -25,13 +25,15 @@
 
     <xml name="annotation_dir">
         <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
-            <options from_file="gemini_databases.loc">
+            <options from_file="gemini_databases">
               <column name="value" index="0"/>
               <column name="dbkey" index="1"/>
               <column name="name" index="2"/>
               <column name="path" index="3"/>
             </options>
+            <filter type="sort_by" column="0" />
             <validator type="unspecified_build" />
+            <validator type="no_options" message="No indexes are available" />
         </param>
     </xml>
 
@@ -94,7 +96,7 @@
         </param>
     </xml>
 
-    <token name="@VERSION@">0.9.1</token>
+    <token name="@VERSION@">0.10.0</token>
 
     <token name="@CITATION@">------
 
--- a/gemini_pathways.xml	Mon Aug 25 03:19:30 2014 -0400
+++ b/gemini_pathways.xml	Mon Aug 25 04:21:34 2014 -0400
@@ -9,7 +9,7 @@
     <command>
 <![CDATA[
         gemini 
-            --annotation-dir ${annotation_databases}
+            --annotation-dir ${annotation_databases.fields.path}
             @BINARY@
             -v $ensembl
             $lof