# HG changeset patch
# User bgruening
# Date 1361735376 18000
# Node ID 73508c5b4273199c0907463c87e5a3405db57735
# Parent  c066c09db337613029766c3de4a3ffc19b588254
Uploaded

diff -r c066c09db337 -r 73508c5b4273 README
--- a/README	Mon Feb 18 16:07:12 2013 -0500
+++ b/README	Sun Feb 24 14:49:36 2013 -0500
@@ -1,8 +1,5 @@
 Bismark uses Bowtie or Bowtie2 to map the reads.
-Create your reference index with bismark_genome_preparation in your
-normal Bowtie2/Botwie index directory. 
-bismark_genome_preparation will create a Bisulfite_Genome folder directly in
-your Bowtie2/Bowtie index directory. If you follow that approach you do not 
-need to specify or modify an extra *.loc file.
-That wrapper will extract the path to the Bisulfite_Genome folder from
-./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
+
+Create your reference index with bismark_genome_preparation in your normal Bowtie2/Botwie index directory. 
+bismark_genome_preparation will create a Bisulfite_Genome folder directly in your Bowtie2/Bowtie index directory. If you follow that approach you do not need to specify or modify an extra *.loc file.
+That wrapper will extract the path to the Bisulfite_Genome folder from ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
diff -r c066c09db337 -r 73508c5b4273 bismark_bowtie_wrapper.xml
--- a/bismark_bowtie_wrapper.xml	Mon Feb 18 16:07:12 2013 -0500
+++ b/bismark_bowtie_wrapper.xml	Sun Feb 24 14:49:36 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie" name="Bismark" version="0.7.7.2">
+<tool id="bismark_bowtie" name="Bismark" version="0.7.7.3">
     <!-- Wrapper compatible with Bismark version 0.7.7 -->
     <description>bisulfite mapper (bowtie)</description>
     <!--<version_command>bismark version</version_command>-->
@@ -73,11 +73,7 @@
             --seed-len $params.seed_len
             ## default 0
             --seed-mismatches $params.seed_mismatches
-            ## default 15
-            --seed-extention-attempts $params.seed_extention_attempts
-            ## default 2
-            --max-reseed $params.max_reseed
-            
+
             ## default 70
             ##--maqerr $params.maqerr
 
@@ -89,12 +85,6 @@
                 --skip-reads $params.skip_reads
             #end if
 
-            ## if set, disable the original behaviour
-            $params.no_mixed
-            ## if set, disable the original behaviour
-            $params.no_discordant
-
-
             ###if str($params.isReportOutput) == "yes":
             ##    --output-report-file $report_file
             ###end if
@@ -186,9 +176,6 @@
                 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
                 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
 
-                <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
-                <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
-
                 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
                 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" />
                 <!-- output Options -->
diff -r c066c09db337 -r 73508c5b4273 bismark_wrapper.py
--- a/bismark_wrapper.py	Mon Feb 18 16:07:12 2013 -0500
+++ b/bismark_wrapper.py	Sun Feb 24 14:49:36 2013 -0500
@@ -178,7 +178,7 @@
 
     if not args.bowtie2:
         # use bowtie specific options
-        additional_opts += ' --best '
+        #additional_opts += ' --best ' # bug in bismark, --best is not available only --non-best, best is default
         if args.seed_mismatches:
             # --seedmms
             additional_opts += ' -n %s ' % args.seed_mismatches