# HG changeset patch
# User iuc
# Date 1544205108 18000
# Node ID f052e48b47835d19f645f7510ba5bc38cf879469
# Parent  54f607ff195b66b2b1a9ae9882735ee305fe7f10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b

diff -r 54f607ff195b -r f052e48b4783 gemini_annotate.xml
--- a/gemini_annotate.xml	Tue Feb 16 05:56:10 2016 -0500
+++ b/gemini_annotate.xml	Fri Dec 07 12:51:48 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.2">
     <description>adding your own custom annotations</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -10,11 +10,15 @@
     <command>
 <![CDATA[
 
-    bgzip -c "$annotate_source" > tabixed.gz &&
-    tabix -p bed tabixed.gz &&
+    ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
+    #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
+    bgzip -c "$annotate_source" > $tabixed_file &&
+    tabix -p "$annotate_source.ext" $tabixed_file &&
+
+        @PROVIDE_ANNO_DATA@
 
         gemini @BINARY@
-            -f tabixed.gz
+            -f $tabixed_file
             -c $column_name
             -a $a.a_selector
             #if $a.a_selector == 'extract':
@@ -30,7 +34,7 @@
     </command>
     <inputs>
         <expand macro="infile" />
-        <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/>
+        <param name="annotate_source" type="data" format="vcf,bed" label="File containing the annotations in BED/VCF format" help="(-f)"/>
 
         <param name="column_name" type="text" value=""
             label="The name of the column to be added to the variant table" 
@@ -45,12 +49,12 @@
             <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)">
                 <option value="boolean">Did a variant overlap a region or not? (boolean)</option>
                 <option value="count">How many regions did a variant overlap? (count)</option>
-                <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option>
+                <option value="extract" selected="True">Extract specific values from a BED/VCF file. (extract)</option>
             </param>
             <when value="extract">
 
-                <param name="column_extracts" label="Column to extract information from for list annotations"
-                    type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/>
+                <param name="column_extracts" label="Column to extract information from for list annotations. For BED files, this is the column number. For VCF files, this is the name of the INFO field."
+                    type="text" force_select="true" help="(-e)"/>
 
 
                 <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?"
diff -r 54f607ff195b -r f052e48b4783 gemini_macros.xml
--- a/gemini_macros.xml	Tue Feb 16 05:56:10 2016 -0500
+++ b/gemini_macros.xml	Fri Dec 07 12:51:48 2018 -0500
@@ -1,7 +1,15 @@
 <macros>
+    <!-- gemini version to be used -->
+    <token name="@VERSION@">0.18.1</token>
+    <!-- minimal annotation files version required by this version of gemini -->
+    <token name="@DB_VERSION@">181</token>
+
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.18.1">gemini</requirement>
+            <requirement type="package" version="@VERSION@">gemini</requirement>
+            <requirement type="package" version="0.2.6">tabix</requirement>
+            <!-- for conda useage -->
+            <!--requirement type="package" version="1.3.1">htslib</requirement-->
             <yield />
         </requirements>
     </xml>
@@ -20,9 +28,10 @@
     </xml>
 
     <xml name="annotation_dir">
-        <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database">
-            <options from_data_table="gemini_databases">
+        <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
+            <options from_data_table="gemini_versioned_databases">
                 <filter type="sort_by" column="0" />
+                <filter type="static_value" column="2" value="@DB_VERSION@" />
             </options>
         </param>
     </xml>
@@ -62,6 +71,7 @@
                     <option value="impact_severity">impact_severity</option>
                     <option value="max_aaf_all">alternative allele frequency</option>
                 </param>
+                <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
             </when>
         </conditional>
     </xml>
@@ -84,14 +94,44 @@
 
     <xml name="sanitize_query">
         <sanitizer invalid_char="">
-            <valid initial="string.printable"/>
+            <valid initial="string.printable">
+                <remove value="&apos;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+            </mapping>
        </sanitizer>
     </xml>
 
+    <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
+        mkdir gemini &&
+        ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data &&
+        export GEMINI_CONFIG="${annotation_databases.fields.path}" &&
+    ]]></token>
+
+    <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
+        #set $sql_expr = str($multiline_sql_expr).strip()
+        #if str($sql_expr):
+            #set $sql_expr = $sql_expr.replace('\r\n', '\n')
+            #set $sql_expr = $sql_expr.replace('\r', '\n')
+            #set $sql_expr = $sql_expr.replace('\\\n', ' ')
+            $cmdln_param '$sql_expr'
+        #end if
+    </token>
+
     <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
         #if str($filter.filter_selector) == 'yes' and $filter.filter:
-            #import pipes
-            --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
+            --filter '${ str( $filter.filter ) }'
+        #end if
+    </token>
+
+    <token name="@COLUMN_SELECT@">
+        #if $report.report_selector != 'all':
+            --columns "${report.columns}
+            #if str($report.extra_cols).strip()
+                #echo ','+','.join(str($report.extra_cols).split()) 
+            #end if
+            "
         #end if
     </token>
 
@@ -125,7 +165,6 @@
     <xml name="gt_pl_max">
         <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />
     </xml>
-    <token name="@VERSION@">0.18.1</token>
 
     <xml name="citations">
         <citations>
diff -r 54f607ff195b -r f052e48b4783 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Feb 16 05:56:10 2016 -0500
+++ b/repository_dependencies.xml	Fri Dec 07 12:51:48 2018 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="eb54ffdea8a0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="8885ab36d6b5" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 54f607ff195b -r f052e48b4783 tool-data/gemini_databases.loc.sample
--- a/tool-data/gemini_databases.loc.sample	Tue Feb 16 05:56:10 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-## GEMINI databases
-#Version	dbkey	Description	Path
-#08_08_2014	hg19	Database (08-08-2014)	/path/to/data
diff -r 54f607ff195b -r f052e48b4783 tool-data/gemini_versioned_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gemini_versioned_databases.loc.sample	Fri Dec 07 12:51:48 2018 -0500
@@ -0,0 +1,3 @@
+## GEMINI versioned databases
+#DownloadDate	dbkey	DBversion	Description	Path
+#2018-07-08	hg19	181	GEMINI annotations (2018-07-08 snapshot)	/path/to/data
diff -r 54f607ff195b -r f052e48b4783 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Feb 16 05:56:10 2016 -0500
+++ b/tool_data_table_conf.xml.sample	Fri Dec 07 12:51:48 2018 -0500
@@ -1,7 +1,7 @@
 <tables>
-    <table name="gemini_databases" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gemini_databases.loc" />
+    <table name="gemini_versioned_databases" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, version, name, path</columns>
+        <file path="tool-data/gemini_versioned_databases.loc" />
     </table>
 </tables>
 
diff -r 54f607ff195b -r f052e48b4783 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 16 05:56:10 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="gemini" version="0.18.1">
-        <repository changeset_revision="13ce32ffda3a" name="package_gemini_0_18_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>