diff datamanager_create_reference.xml @ 41:74de1ccc51db

Add GRCh38 hg38, minor fixes.

--- a/datamanager_create_reference.xml	Wed May 06 14:31:57 2015 -0500
+++ b/datamanager_create_reference.xml	Fri Dec 18 14:37:33 2015 -0600
@@ -17,6 +17,7 @@
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
+      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
       <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>
       <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
       <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
@@ -24,6 +25,20 @@
       <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
       <option value="user_specified">User specified</option>
     </param>
+    <when value="GRCh38">
+      <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
+      <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
+      <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
+      <param name="ensembl_version" type="hidden" value="80"/>
+      <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
+      <param name="ncbi_prefix" type="hidden" value="Hs"/>
+      <param name="ucsc_genome_version" type="hidden" value="hg38"/>
+      <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
+      <param name="mt_chromosome" type="hidden" value="MT"/>
+      <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
+      <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
+      <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
+    </when>
     <when value="GRCh37">
       <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
       <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
@@ -221,6 +236,9 @@
 gene_sources = $genome.gene_sources
 ig_gene_sources = $genome.ig_gene_sources
 rrna_gene_sources = $genome.rrna_gene_sources
+gene_biotypes = $genome.gene_sources
+ig_gene_biotypes = $genome.ig_gene_sources
+rrna_gene_biotypes = $genome.rrna_gene_sources
 
 #raw
 # Remove temp files
@@ -228,7 +246,7 @@
 remove_job_temp_files                       = yes
 #end raw
   </configfile>
-  <configfile name="defuse_script">
+  <configfile name="defuse_script">#slurp
 #!/bin/bash
 ## define some things for cheetah proccessing
 #set $amp = chr(38)