--- a/segemehl.xml	Sat Feb 22 06:01:16 2014 -0500
+++ b/segemehl.xml	Wed Feb 04 06:52:06 2015 -0500
@@ -4,18 +4,19 @@
         <requirement type="package" version="0.1.6">segemehl</requirement>
     </requirements>
     <command>
+<![CDATA[
         ## prepare segemehl index if no reference genome is supplied
         temp_index = `mktemp`;
         #if $refGenomeSource.genomeSource == "history":
             segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome;
         #else:
-            $temp_index = ${refGenomeSource.index.fields.index_path}
+            #set $temp_index = ${refGenomeSource.index.fields.index_path}
         #end if
 
 
         ## execute segemehl
         segemehl.x
-        
+
         ## number of threads
         -t "\${GALAXY_SLOTS:-12}"
 
@@ -34,7 +35,7 @@
             -q "#echo ' '.join( $query_list )#"
         #else
             ## prepare inputs
-            
+
             #set $mate1 = list()
             #set $mate2 = list()
             #for $mate_pair in $library.mate_list:
@@ -62,11 +63,12 @@
         $order
         -s
         -o $segemehl_out
+]]>
     </command>
     <stdio>
-        <regex match="Exit forced" 
-           source="both" 
-           level="fatal" 
+        <regex match="Exit forced"
+           source="both"
+           level="fatal"
            description="Execution halted." />
     </stdio>
     <inputs>
@@ -137,24 +139,25 @@
         <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/>
     </outputs>
     <help>
+<![CDATA[
 
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 Segemehl_ is a short read mapper with gaps.
 
-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_ 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_ 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>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1000502</citation>
+    </citations>
 </tool>