# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1381874543 18000
# Node ID 3099cec648e7b9f8cdd338ddeab3c5497ca0a781
# Parent  3e3ebdecb0e1fe62ea6fb92ef33f03c7e90a2d72
Update tool_dependencies, add help

diff -r 3e3ebdecb0e1 -r 3099cec648e7 create_reference_dataset.xml
--- a/create_reference_dataset.xml	Fri Sep 06 08:20:41 2013 -0500
+++ b/create_reference_dataset.xml	Tue Oct 15 17:02:23 2013 -0500
@@ -89,7 +89,12 @@
       <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
     </when>
     <when value="user_specified">
-      <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
+      <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name">
+       <help>
+       Examples: homo_sapiens, mus_musculus, rattus_norvegicus
+       ftp://ftp.ensembl.org/pub/release-$ensembl_version/fasta/$ensembl_organism/dna/$ensembl_prefix.$ensembl_genome_version.$ensembl_version.dna.chromosome.$chromosome.fa.gz
+       </help>
+       </param>
       <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
       <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
       <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
diff -r 3e3ebdecb0e1 -r 3099cec648e7 defuse_results_to_vcf.py
--- a/defuse_results_to_vcf.py	Fri Sep 06 08:20:41 2013 -0500
+++ b/defuse_results_to_vcf.py	Tue Oct 15 17:02:23 2013 -0500
@@ -97,6 +97,8 @@
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate">
+##INFO=<ID=MATELOC,Number=1,Type=String,Description="The chrom:position of the BND mate">
+##INFO=<ID=GENESTRAND,Number=2,Type=String,Description="Strands">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
 ##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction">
 ##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion">
@@ -255,8 +257,8 @@
         info.append('EVERSION')
       if inversion:
         info.append('INVERSION')
-      info1 = [svtype,'MATEID=%s' % mate_id2] + info
-      info2 = [svtype,'MATEID=%s' % mate_id1] + info
+      info1 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id2,gene_chromosome2,genomic_break_pos2)] + info
+      info2 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id1,gene_chromosome1,genomic_break_pos1)] + info
       qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.'
       vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) )
       vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) )
@@ -265,7 +267,7 @@
     write_vcf()
   except Exception, e:
     print >> sys.stderr, "failed: %s" % e
-    exit(1)
+    sys.exit(1)
 
 if __name__ == "__main__" : __main__()
 
diff -r 3e3ebdecb0e1 -r 3099cec648e7 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 06 08:20:41 2013 -0500
+++ b/tool_dependencies.xml	Tue Oct 15 17:02:23 2013 -0500
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="defuse" version="0.6.1">
-        <repository changeset_revision="370c0672e531" name="package_defuse_0_6_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="66cb7175c473" name="package_defuse_0_6_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="06697b4877f9" name="package_samtools_0_1_19" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.0.0">
         <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />