Add bam.iobio as a display application.

galaxyproject · Mar 15, 2016 · 46728c5 · 46728c5
1 parent 23c3300
commit 46728c5
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Showing 5 changed files with 18 additions and 1 deletion.
diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
@@ -15,6 +15,7 @@
       <display file="ensembl/ensembl_bam.xml" />
       <display file="igv/bam.xml" />
       <display file="igb/bam.xml" />
+      <display file="iobio/bam.xml" />
     </datatype>
     <datatype extension="cram" type="galaxy.datatypes.binary:CRAM" mimetype="application/octet-stream" display_in_upload="true" description="CRAM is a file format for highly efficient and tunable reference-based compression of alignment data." description_url="http://www.ebi.ac.uk/ena/software/cram-usage"/>
     <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed">

diff --git a/config/tool_data_table_conf.xml.sample b/config/tool_data_table_conf.xml.sample
@@ -75,4 +75,9 @@
         <columns>dbkey, name, value</columns>
         <file path="tool-data/liftOver.loc" />
     </table>
+    <!-- iobio bam servers -->
+    <table name="bam_iobio" comment_char="#">
+        <columns>value, name, url</columns>
+        <file path="tool-data/bam_iobio.loc" />
+    </table>
 </tables>
diff --git a/display_applications/iobio/bam.xml b/display_applications/iobio/bam.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<display id="iobio_bam" version="1.0.0" name="display at bam.iobio">
+    <dynamic_links from_data_table="bam_iobio" skip_startswith="#" id="value" name="name">
+        <url>${url}?bam=${bam_file.qp}</url>
+        <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
+        <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
+    </dynamic_links>
+</display>
diff --git a/lib/galaxy/datatypes/display_applications/application.py b/lib/galaxy/datatypes/display_applications/application.py
@@ -142,7 +142,7 @@ def __init__( self, elem, display_application, build_sites ):
         max_col = max( id_col, name_col )
         dynamic_params = {}
         if data_table is not None:
-            max_col = max(  [ max_col ] + data_table.columns.values() )
+            max_col = max( [ max_col ] + data_table.columns.values() )
             for key, value in data_table.columns.items():
                 dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
         for dynamic_param in elem.findall( 'dynamic_param' ):

diff --git a/tool-data/bam_iobio.loc.sample b/tool-data/bam_iobio.loc.sample
@@ -0,0 +1,3 @@
+# Table used for listing bam.iobio servers
+#<unique_id>	<display_name>	<url>
+bam_iobio	bam.iobio.io	http://bam.iobio.io/