# HG changeset patch
# User bjoern-gruening
# Date 1362163162 18000
# Node ID 427fb56f2e41bb2c744e45ea44dc2d5c36c6ff73
# Parent  7eefe5d6eecd9ee4acebfb14a0d96768a97fe047
- new options
- fixes

diff -r 7eefe5d6eecd -r 427fb56f2e41 README
--- a/README	Tue Dec 25 05:54:01 2012 -0500
+++ b/README	Fri Mar 01 13:39:22 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 7eefe5d6eecd -r 427fb56f2e41 bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml	Tue Dec 25 05:54:01 2012 -0500
+++ b/bismark_bowtie2_wrapper.xml	Fri Mar 01 13:39:22 2013 -0500
@@ -12,7 +12,7 @@
         bismark_wrapper.py
         
         ## Change this to accommodate the number of threads you have available.
-        --num-threads 4
+        --num-threads 12
 
         --bismark_path \$SCRIPT_PATH
 
@@ -47,16 +47,23 @@
                 --fasta
             #end if
         #else:
-            --mate-paired 
-            --mate1 $singlePaired.input_mate1
-            --mate2 $singlePaired.input_mate2
+            --mate-paired
+            #set $mate1 = list()
+            #set $mate2 = list()
+            #for $mate_pair in $singlePaired.mate_list
+                $mate1.append( str($mate_pair.input_mate1) )
+                $mate2.append( str($mate_pair.input_mate2) )
+            #end for
 
-            #if $singlePaired.input_mate1.ext == "fastqillumina":
+            --mate1 #echo ','.join($mate1)
+            --mate2 #echo ','.join($mate2)
+
+            #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
                 --phred64-quals
                 --fastq
-            #elif $singlePaired.input_mate1.ext == "fastqsanger":
+            #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
                 --fastq
-            #elif $singlePaired.input_mate1.ext == "fasta":
+            #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
                 --fasta
             #end if
 
@@ -157,8 +164,10 @@
                 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
+                <repeat name="mate_list" title="Paired End Pairs" min="1">
+                    <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
+                    <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
+                </repeat>
                 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
             </when>
@@ -247,7 +256,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -267,7 +276,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -291,7 +300,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -310,7 +319,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -353,6 +362,11 @@
 
  .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
 
+
+.. class:: warningmark
+
+Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.
+
 ------
 
 **Input formats**
@@ -415,12 +429,7 @@
 
 **Bismark parameter list**
 
-This is an exhaustive list of Bismark options:
-
-------
-
-**OPTIONS**
-
+This is an exhaustive list of Bismark options.
 
 Input::
 
diff -r 7eefe5d6eecd -r 427fb56f2e41 bismark_bowtie_wrapper.xml
--- a/bismark_bowtie_wrapper.xml	Tue Dec 25 05:54:01 2012 -0500
+++ b/bismark_bowtie_wrapper.xml	Fri Mar 01 13:39:22 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>-->
@@ -10,9 +10,6 @@
     <parallelism method="basic"></parallelism>
     <command interpreter="python">
         bismark_wrapper.py
-        
-        ## Change this to accommodate the number of threads you have available.
-        --num-threads 4
 
         --bismark_path \$SCRIPT_PATH
 
@@ -45,16 +42,23 @@
                 --fasta
             #end if
         #else:
-            --mate-paired 
-            --mate1 $singlePaired.input_mate1
-            --mate2 $singlePaired.input_mate2
+            --mate-paired
+            #set $mate1 = list()
+            #set $mate2 = list()
+            #for $mate_pair in $singlePaired.mate_list
+                $mate1.append( str($mate_pair.input_mate1) )
+                $mate2.append( str($mate_pair.input_mate2) )
+            #end for
 
-            #if $singlePaired.input_mate1.ext == "fastqillumina":
+            --mate1 #echo ','.join($mate1)
+            --mate2 #echo ','.join($mate2)
+
+            #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
                 --phred64-quals
                 --fastq
-            #elif $singlePaired.input_mate1.ext == "fastqsanger":
+            #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
                 --fastq
-            #elif $singlePaired.input_mate1.ext == "fasta":
+            #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
                 --fasta
             #end if
 
@@ -73,11 +77,7 @@
             --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 +89,6 @@
                 --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
@@ -155,8 +149,10 @@
                 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
+                <repeat name="mate_list" title="Paired End Pairs" min="1">
+                    <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
+                    <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
+                </repeat>
                 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
             </when>
@@ -186,9 +182,6 @@
                 <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 -->
@@ -245,7 +238,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -265,7 +258,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -289,7 +282,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -308,7 +301,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -351,6 +344,11 @@
 
  .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
 
+
+.. class:: warningmark
+
+Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.
+
 ------
 
 **Input formats**
@@ -413,12 +411,7 @@
 
 **Bismark parameter list**
 
-This is an exhaustive list of Bismark options:
-
-------
-
-**OPTIONS**
-
+This is an exhaustive list of Bismark options.
 
 Input::
 
@@ -539,76 +532,5 @@
                          the specified folder does not exist, Bismark will attempt to create it first. The path to the
                          temporary folder can be either relative or absolute.
 
-------
-
-Bowtie 2 alignment options::
-
-  -N INT                 Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
-                         Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
-                         but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -n).
-
-  -L INT                   Sets the length of the seed substrings to align during multiseed alignment. Smaller values
-                         make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
-                         used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -l).
-
-  --ignore-quals         When calculating a mismatch penalty, always consider the quality value at the mismatched
-                         position to be the highest possible, regardless of the actual value. I.e. input is treated
-                         as though all quality values are high. This is also the default behavior when the input
-                         doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
-
-
-Bowtie 2 paired-end options::
-
-  --no-mixed             This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
-                         it cannot find a concordant or discordant alignment for a pair. This option is invariable and
-                         and on by default.
-
-  --no-discordant        Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
-                         A discordant alignment is an alignment where both mates align uniquely, but that does not
-                         satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
-                         and it is on by default.
-
-
-Bowtie 2 effort options::
-
-  -D INT                 Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
-                         the alignments found so far. A seed extension "fails" if it does not yield a new best or a
-                         new second-best alignment. Default: 15.
-
-  -R INT                 INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
-                         When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
-                         mismatches allowed) at different offsets and searches for more alignments. A read is considered
-                         to have repetitive seeds if the total number of seed hits divided by the number of seeds
-                         that aligned at least once is greater than 300. Default: 2.
-
-
-Bowtie 2 Scoring options::
-
-  --score_min "func"     Sets a function governing the minimum alignment score needed for an alignment to be considered
-                         "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
-                         L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
-                         See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
-                         L,0,-0.2.
-
-
-Bowtie 2 Reporting options::
-
- --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
-                         deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
-                         default mode, but adjusting the -M setting is deprecated.  Use the -D and -R options to adjust the
-                         effort expended to find valid alignments.
-
-                         For reference, this used to be the old (now deprecated) description of -M:
-                         Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
-                         can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
-                         happens first. Only the best alignment is reported. Information from the other alignments is used to
-                         estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes 
-                         Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
-                         aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
-                         guarantee that the alignment reported is the best possible in terms of alignment score. -M is
-                         always used and its default value is set to 10.
-
   </help>
 </tool>
diff -r 7eefe5d6eecd -r 427fb56f2e41 bismark_methylation_extractor.py
--- a/bismark_methylation_extractor.py	Tue Dec 25 05:54:01 2012 -0500
+++ b/bismark_methylation_extractor.py	Fri Mar 01 13:39:22 2013 -0500
@@ -25,6 +25,8 @@
     parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')
 
     # input options
+    parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )
+
     parser.add_argument( '--infile', help='Input file in SAM format.' )
     parser.add_argument( '--single-end', dest='single_end', action="store_true" )
     parser.add_argument( '--paired-end', dest='paired_end', action="store_true" )
@@ -70,6 +72,9 @@
     # Build methylation extractor command
     output_dir = tempfile.mkdtemp()
     cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'
+    if args.bismark_path:
+        # add the path to the bismark perl scripts, that is needed for galaxy
+        cmd = os.path.join(args.bismark_path, cmd)
 
     additional_opts = ''
     # Set up all options
diff -r 7eefe5d6eecd -r 427fb56f2e41 bismark_wrapper.py
--- a/bismark_wrapper.py	Tue Dec 25 05:54:01 2012 -0500
+++ b/bismark_wrapper.py	Fri Mar 01 13:39:22 2013 -0500
@@ -119,8 +119,12 @@
         else:
             cmd_index = 'bismark_genome_preparation %s ' % ( tmp_index_dir )
         if args.bismark_path:
-            # add the path to the bismark perl scripts, that is needed for galaxy
-            cmd_index = '%s/%s' % (args.bismark_path, cmd_index)
+            if os.path.exists(args.bismark_path):
+                # add the path to the bismark perl scripts, that is needed for galaxy
+                cmd_index = os.path.join(args.bismark_path, cmd_index)
+            else:
+                # assume the same directory as that script
+                cmd_index = 'perl %s' % os.path.join(os.path.realpath(os.path.dirname(__file__)), cmd_index)
         try:
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
             tmp_stderr = open( tmp, 'wb' )
@@ -147,15 +151,27 @@
             stop_err( 'Error indexing reference sequence\n' + str( e ) )
         index_dir = tmp_index_dir
     else:
-        index_dir = args.index_path
+        # bowtie path is the path to the index directory and the first path of the index file name
+        index_dir = os.path.dirname( args.index_path )
 
     # Build bismark command
     tmp_bismark_dir = tempfile.mkdtemp()
     output_dir = os.path.join( tmp_bismark_dir, 'results')
     cmd = 'bismark %(args)s --temp_dir %(tmp_bismark_dir)s -o %(output_dir)s --quiet %(genome_folder)s %(reads)s'
+
+    if args.fasta:
+        # he query input files (specified as mate1,mate2 or singles) are FastA
+        cmd = '%s %s' % (cmd, '--fasta')
+    elif args.fastq:
+        cmd = '%s %s' % (cmd, '--fastq')
+
     if args.bismark_path:
         # add the path to the bismark perl scripts, that is needed for galaxy
-        cmd = '%s/%s' % (args.bismark_path, cmd)
+        if os.path.exists(args.bismark_path):
+            cmd = os.path.join(args.bismark_path, cmd)
+        else:
+            # assume the same directory as that script
+            cmd = 'perl %s' % os.path.join(os.path.realpath(os.path.dirname(__file__)), cmd)
 
     arguments = {
         'genome_folder': index_dir,
@@ -178,7 +194,7 @@
 
     if not args.bowtie2:
         # use bowtie specific options
-        additional_opts += ' --best '
+        #additional_opts += ' --best ' # bug in bismark, --best is not available as option. Only --non-best, best-mode is activated by default
         if args.seed_mismatches:
             # --seedmms
             additional_opts += ' -n %s ' % args.seed_mismatches