Merge pull request #1926 from blankenberg/iobio-display

Add iobio external display applications for BAM and VCF.

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">
@@ -247,6 +248,7 @@
       <display file="ucsc/vcf.xml" />
       <display file="igv/vcf.xml" />
       <display file="rviewer/vcf.xml" inherit="True"/>
+      <display file="iobio/vcf.xml" />
     </datatype>
     <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="True">
       <converter file="bcf_to_bcf_bgzip_converter.xml" target_datatype="bcf_bgzip"/>

config/tool_data_table_conf.xml.sample

@@ -75,4 +75,14 @@
         <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>
+    <!-- iobio vcf servers -->
+    <table name="vcf_iobio" comment_char="#">
+        <columns>value, name, url</columns>
+        <file path="tool-data/vcf_iobio.loc" />
+    </table>
 </tables>

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>

display_applications/iobio/vcf.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<display id="iobio_vcf" version="1.0.0" name="display at vcf.iobio">
+    <dynamic_links from_data_table="vcf_iobio" skip_startswith="#" id="value" name="name">
+        <url>${url}?vcf=${bgzip_file.qp}</url>
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+    </dynamic_links>
+</display>

lib/galaxy/datatypes/display_applications/application.py

@@ -142,7 +142,7 @@ class DynamicDisplayApplicationBuilder( object ):
         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' ):

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/

tool-data/vcf_iobio.loc.sample

@@ -0,0 +1,3 @@
+# Table used for listing vcf.iobio servers
+#<unique_id>	<display_name>	<url>
+vcf_iobio	vcf.iobio.io	http://vcf.iobio.io/