changeset 2:8da05bf2b1d1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

--- a/gemini_annotate.xml	Tue Mar 22 21:42:26 2016 -0400
+++ b/gemini_annotate.xml	Thu Nov 09 13:18:45 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
     <description>adding your own custom annotations</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -10,11 +10,13 @@
     <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 &&
 
         gemini @BINARY@
-            -f tabixed.gz
+            -f $tabixed_file
             -c $column_name
             -a $a.a_selector
             #if $a.a_selector == 'extract':
@@ -30,7 +32,7 @@
     </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 +47,12 @@
             <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?"

--- a/gemini_macros.xml	Tue Mar 22 21:42:26 2016 -0400
+++ b/gemini_macros.xml	Thu Nov 09 13:18:45 2017 -0500
@@ -3,6 +3,8 @@
         <requirements>
             <requirement type="package" version="0.18.1">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>
@@ -63,6 +65,7 @@
                     <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>
@@ -96,6 +99,16 @@
         #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>
+
     <xml name="family">
         <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
     </xml>

--- a/repository_dependencies.xml	Tue Mar 22 21:42:26 2016 -0400
+++ b/repository_dependencies.xml	Thu Nov 09 13:18:45 2017 -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="345412d58d75" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="172815da3d41" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>

--- a/tool_data_table_conf.xml.sample	Tue Mar 22 21:42:26 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Thu Nov 09 13:18:45 2017 -0500
@@ -1,5 +1,5 @@
 <tables>
-    <table name="gemini_databases" comment_char="#">
+    <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gemini_databases.loc" />
     </table>