# HG changeset patch
# User bgruening
# Date 1390040791 18000
# Node ID 468b59eae694612374e73e3377fa384440ce5db2
# Parent  94926c35b6f37cda5756abdeeb1a0332ba6278da
Uploaded

diff -r 94926c35b6f3 -r 468b59eae694 segemehl.xml
--- a/segemehl.xml	Thu Oct 17 04:07:29 2013 -0400
+++ b/segemehl.xml	Sat Jan 18 05:26:31 2014 -0500
@@ -1,5 +1,5 @@
-<tool id="segemehl" name="segemehl" version="0.1">
-    <description>suffix arrays based short read aligner</description>
+<tool id="segemehl" name="segemehl" version="0.1.6.0">
+    <description>based short read aligner</description>
     <requirements>
         <requirement type="package" version="0.1.6">segemehl</requirement>
     </requirements>
@@ -17,7 +17,7 @@
         segemehl.x
         
         ## number of threads
-        -t 4
+        -t "\${GALAXY_SLOTS:-12}"
 
         ## db file path
         -d ${refGenomeSource.index.fields.db_path}
@@ -139,13 +139,19 @@
 
 **What it does** 
 
-Segemelt is a short read mapper with gaps.
+Segemehl_ is a short read mapper with gaps.
 
-segemehl is a software to map short sequencer reads to reference genomes. 
+Segemehl_ is a software to map short sequencer reads to reference genomes. 
 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. 
 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. 
-segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, 
-reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.
+segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
+
+.. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+
+**References**
+
+Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502
+download latest version: 0.1.6 manual: download here new stuff: faster multiple split read mapping bug fixes: bugfixes: increased sensitivity for strand switches changes: - default accuracy now 90% older segemehl indices are still usable. issues: untraceable errors with gcc compiler gcc-4.5. zlib linker problems with some ubuntu versions complaint department: steve bioinf uni leipzig deshapeimage_1_link_0shapeimage_1_link_1
 
     </help>
 </tool>
diff -r 94926c35b6f3 -r 468b59eae694 tool-data/segemehl_indices.loc.sample
--- a/tool-data/segemehl_indices.loc.sample	Thu Oct 17 04:07:29 2013 -0400
+++ b/tool-data/segemehl_indices.loc.sample	Sat Jan 18 05:26:31 2014 -0500
@@ -25,6 +25,5 @@
 #
 #hg18canon          hg18   hg18 Canonical   /data/0/galaxy/segemehl/hg18/chromosomes_can.fa   /data/0/galaxy/segemehl/hg18/chromosomes_can.idx
 #hg18full           hg18   hg18 Full        /data/0/galaxy/segemehl/hg18/chromosomes_full.fa   /data/0/galaxy/segemehl/hg18/chromosomes_full.idx
-#/orig/path/hg19    hg19   hg19             /data/0/galaxy/segemehl/hg19/chromosomes.fa   /data/0/galaxy/segemehl/hg19/chromosomes.idx
 #...etc...
 #
diff -r 94926c35b6f3 -r 468b59eae694 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Oct 17 04:07:29 2013 -0400
+++ b/tool_dependencies.xml	Sat Jan 18 05:26:31 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="segemehl" version="0.1.6">
-        <repository changeset_revision="15c10db35624" name="package_segemehl_0_1_6" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e9455aa5c7e6" name="package_segemehl_0_1_6" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>