changeset 4:ca4449689d61 draft

Uploaded

--- a/gemini_interactions.xml	Sun Aug 24 17:50:00 2014 -0400
+++ b/gemini_interactions.xml	Mon Aug 25 03:19:30 2014 -0400
@@ -9,6 +9,7 @@
     <command>
 <![CDATA[
         gemini 
+            --annotation-dir ${annotation_databases}
             #if $gene.gene_selector == 'lof':
                 ## lof interactions is a separate program
                 lof_interactions
@@ -38,6 +39,7 @@
             </when>
             <when value="lof"/>
         </conditional>
+        <expand macro="annotation_dir" />
         <expand macro="radius" />
         <expand macro="variant_mode" />
     </inputs>

--- a/gemini_load.xml	Sun Aug 24 17:50:00 2014 -0400
+++ b/gemini_load.xml	Mon Aug 25 03:19:30 2014 -0400
@@ -8,7 +8,9 @@
     </macros>
     <command>
 <![CDATA[
-        gemini @BINARY@
+        gemini 
+            --annotation-dir ${annotation_databases}
+            @BINARY@
             -v "${ infile }"
             -t $annotation_type
 
@@ -36,6 +38,7 @@
             <option value="VEP">VEP annotated VCF file</option>
         </param>
         <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
+        <expand macro="annotation_dir" />
 
         <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False" 
             label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>

--- a/gemini_macros.xml	Sun Aug 24 17:50:00 2014 -0400
+++ b/gemini_macros.xml	Mon Aug 25 03:19:30 2014 -0400
@@ -23,6 +23,18 @@
         </stdio>
     </xml>
 
+    <xml name="annotation_dir">
+        <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
+            <options from_file="gemini_databases.loc">
+              <column name="value" index="0"/>
+              <column name="dbkey" index="1"/>
+              <column name="name" index="2"/>
+              <column name="path" index="3"/>
+            </options>
+            <validator type="unspecified_build" />
+        </param>
+    </xml>
+
     <xml name="add_header_column">
         <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" 
             label="Add a header of column names to the output" help="(--header)"/>

--- a/gemini_pathways.xml	Sun Aug 24 17:50:00 2014 -0400
+++ b/gemini_pathways.xml	Mon Aug 25 03:19:30 2014 -0400
@@ -8,7 +8,9 @@
     </macros>
     <command>
 <![CDATA[
-        gemini @BINARY@
+        gemini 
+            --annotation-dir ${annotation_databases}
+            @BINARY@
             -v $ensembl
             $lof
             "${ infile }"
@@ -26,7 +28,7 @@
 
         <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False" 
             label="Report only pathways with loss-of-function variants" help="(--lof)"/>
-
+        <expand macro="annotation_dir" />
     </inputs>
     <outputs>
         <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gemini_databases.loc.sample	Mon Aug 25 03:19:30 2014 -0400
@@ -0,0 +1,3 @@
+## GEMINI databases
+#Version	dbkey	Description
+#08_08_2014	hg19	Database (08-08-2014)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Aug 25 03:19:30 2014 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <table name="gemini_databases" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gemini_databases.loc" />
+    </table>
+</tables>
+