Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.

lib/galaxy/datatypes/binary.py

@@ -7,7 +7,7 @@ from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes import metadata
 from galaxy.datatypes.sniff import *
 from urllib import urlencode, quote_plus
-import zipfile
+import zipfile, gzip
 import os, subprocess, tempfile
 
 log = logging.getLogger(__name__)
@@ -54,32 +54,35 @@ class Bam( Binary ):
 
     def init_meta( self, dataset, copy_from=None ):
         Binary.init_meta( self, dataset, copy_from=copy_from )
-        """
-        GVK 12/2/09: just noticed this - not good and doesn't work, so commenting out for now.
-        def set_meta( self, dataset, overwrite = True, **kwd ):
-            # Sets index for BAM file.
-            index_file = dataset.metadata.bam_index
-            if not index_file:
-                index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+    def set_meta( self, dataset, overwrite = True, **kwd ):
+        """ Sets index for BAM file. """
+        # These metadata values are not accessible by users, always overwrite
+        index_file = dataset.metadata.bam_index
+        if not index_file:
+            index_file = dataset.metadata.spec['bam_index'].param.new_file( dataset = dataset )
+        try:
+            # Using a symlink from ~/database/files/dataset_XX.dat, create a temporary file
+            # to store the indexex generated from samtools, something like ~/tmp/dataset_XX.dat.bai
             tmp_dir = tempfile.gettempdir()
-            tmpf1 = tempfile.NamedTemporaryFile( dir=tmp_dir )
-            tmpf1bai = '%s.bai' % tmpf1.name
-            try:
-                os.system( 'cd %s' % tmp_dir )
-                os.system( 'cp %s %s' % ( dataset.file_name, tmpf1.name ) )
-                os.system( 'samtools index %s' % tmpf1.name )
-                os.system( 'cp %s %s' % ( tmpf1bai, index_file.file_name ) )
-            except Exception, ex:
-                sys.stderr.write( 'There was a problem creating the index for the BAM file\n%s\n' + str( ex ) )
-            tmpf1.close()
-            if os.path.exists( tmpf1bai ):
-                os.remove( tmpf1bai )
-            dataset.metadata.bam_index = index_file
-        """
+            tmp_file_path = os.path.join( tmp_dir, os.path.basename( dataset.file_name ) )
+            # Here tmp_file_path looks something like /tmp/dataset_XX.dat
+            os.symlink( dataset.file_name, tmp_file_path )
+            command = 'samtools index %s' % tmp_file_path
+            proc = subprocess.Popen( args=command, shell=True )
+            proc.wait()
+        except:
+            err_msg = 'Error creating index file (%s) for BAM file (%s)' % ( str( tmp_file_path ), str( dataset.file_name ) )
+            log.exception( err_msg )
+            sys.stderr.write( err_msg )
+        # Move the temporary index file ~/tmp/dataset_XX.dat.bai to be ~/database/files/_metadata_files/dataset_XX.dat
+        shutil.move( '%s.bai' % ( tmp_file_path ), index_file.file_name )
+        os.unlink( tmp_file_path )
+        dataset.metadata.bam_index = index_file
     def sniff( self, filename ):
+        # BAM is compressed in the BGZF format, and must not be uncompressed in Galaxy.
         # The first 4 bytes of any bam file is 'BAM\1', and the file is binary. 
         try:
-            header = open( filename ).read(4)
+            header = gzip.open( filename ).read(4)
             if binascii.b2a_hex( header ) == binascii.hexlify( 'BAM\1' ):
                 return True
             return False

lib/galaxy/tools/util/maf_utilities.py

@@ -191,13 +191,16 @@ def open_or_build_maf_index( maf_file, index_filename, species = None ):
 def build_maf_index_species_chromosomes( filename, index_species = None ):
     species = []
     species_chromosomes = {}
-    indexes = bx.interval_index_file.Indexes()
+    indexes = bx.interval_index_file.Indexes()
+    blocks = 0
     try:
         maf_reader = bx.align.maf.Reader( open( filename ) )
         while True:
             pos = maf_reader.file.tell()
             block = maf_reader.next()
-            if block is None: break
+            if block is None:
+                break
+            blocks += 1
             for c in block.components:
                 spec = c.src
                 chrom = None
@@ -225,11 +228,11 @@ def build_maf_index_species_chromosomes( filename, index_species = None ):
         #most likely a bad MAF
         log.debug( 'Building MAF index on %s failed: %s' % ( filename, e ) )
         return ( None, [], {} )
-    return ( indexes, species, species_chromosomes )
+    return ( indexes, species, species_chromosomes, blocks )
 
 #builds and returns ( index, index_filename ) for specified maf_file
 def build_maf_index( maf_file, species = None ):
-    indexes, found_species, species_chromosomes = build_maf_index_species_chromosomes( maf_file, species )
+    indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes( maf_file, species )
     if indexes is not None:
         fd, index_filename = tempfile.mkstemp()
         out = os.fdopen( fd, 'w' )

tools/data_source/data_source.py

@@ -12,6 +12,7 @@ def stop_err( msg ):
     sys.exit()
 
 def check_gzip( filename ):
+    # TODO: This needs to check for BAM files since they are compressed and must remain so ( see upload.py )
     temp = open( filename, "U" )
     magic_check = temp.read( 2 )
     temp.close()
@@ -66,6 +67,7 @@ def __main__():
         out.write( chunk )
     out.close()
     if check_gzip( filename ):
+        # TODO: This needs to check for BAM files since they are compressed and must remain so ( see upload.py )
         fd, uncompressed = tempfile.mkstemp()
         gzipped_file = gzip.GzipFile( filename )
         while 1:

tools/data_source/upload.py

@@ -4,7 +4,7 @@
 # WARNING: Changes in this tool (particularly as related to parsing) may need
 # to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
 
-import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs
+import urllib, sys, os, gzip, tempfile, shutil, re, gzip, zipfile, codecs, binascii
 from galaxy import eggs
 # need to import model before sniff to resolve a circular import dependency
 import galaxy.model
@@ -18,7 +18,6 @@ assert sys.version_info[:2] >= ( 2, 4 )
 def stop_err( msg, ret=1 ):
     sys.stderr.write( msg )
     sys.exit( ret )
-
 def file_err( msg, dataset, json_file ):
     json_file.write( to_json_string( dict( type = 'dataset',
                                            ext = 'data',
@@ -28,7 +27,6 @@ def file_err( msg, dataset, json_file ):
         os.remove( dataset.path )
     except:
         pass
-
 def safe_dict(d):
     """
     Recursively clone json structure with UTF-8 dictionary keys
@@ -40,7 +38,6 @@ def safe_dict(d):
         return [safe_dict(x) for x in d]
     else:
         return d
-
 def check_html( temp_name, chunk=None ):
     if chunk is None:
         temp = open(temp_name, "U")
@@ -64,7 +61,6 @@ def check_html( temp_name, chunk=None ):
     if chunk is None:
         temp.close()
     return False
-
 def check_binary( temp_name, chunk=None ):
     if chunk is None:
         temp = open( temp_name, "U" )
@@ -85,21 +81,42 @@ def check_binary( temp_name, chunk=None ):
     if chunk is None:
         temp.close()
     return False
-
 def check_gzip( temp_name ):
+    # This is sort of hacky.  BAM is compressed in the BGZF format, and must 
+    # not be uncompressed in upon upload ( it will be detected as gzipped ).
+    # The tuple we're returning from here contains boolean values for
+    # ( is_compressed, is_valid, is_bam ).
     temp = open( temp_name, "U" )
     magic_check = temp.read( 2 )
     temp.close()
     if magic_check != util.gzip_magic:
-        return ( False, False )
+        return ( False, False, False )
     CHUNK_SIZE = 2**15 # 32Kb
     gzipped_file = gzip.GzipFile( temp_name )
     chunk = gzipped_file.read( CHUNK_SIZE )
     gzipped_file.close()
-    if check_html( temp_name, chunk=chunk ) or check_binary( temp_name, chunk=chunk ):
-        return( True, False )
-    return ( True, True )
-
+    if check_html( temp_name, chunk=chunk ):
+        return ( True, False, False )
+    if check_binary( temp_name, chunk=chunk ):
+        # We do support some binary data types, so check if the compressed binary file is valid
+        # We currently only check for [ 'sff', 'bam' ]
+        # TODO: this should be fixed to more easily support future-supported binary data types.
+        # This is currently just copied from the sniff methods.
+        # The first 4 bytes of any bam file is 'BAM\1', and the file is binary. 
+        try:
+            header = gzip.open( temp_name ).read(4)
+            if binascii.b2a_hex( header ) == binascii.hexlify( 'BAM\1' ):
+                return ( True, True, True )
+        except:
+            pass
+        try:
+            header = gzip.open( temp_name ).read(4)
+            if binascii.b2a_hex( header ) == binascii.hexlify( '.sff' ):
+                return ( True, True, False )
+        except:
+            pass
+        return ( True, False, False )
+    return ( True, True, False )
 def check_zip( temp_name ):
     if not zipfile.is_zipfile( temp_name ):
         return ( False, False, None )
@@ -116,14 +133,12 @@ def check_zip( temp_name ):
         if ext != test_ext:
             return ( True, False, test_ext )
     return ( True, True, test_ext )
-
 def parse_outputs( args ):
     rval = {}
     for arg in args:
         id, files_path, path = arg.split( ':', 2 )
         rval[int( id )] = ( path, files_path )
     return rval
-
 def add_file( dataset, json_file, output_path ):
     data_type = None
     line_count = None
@@ -153,15 +168,19 @@ def add_file( dataset, json_file, output_path ):
         ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
     else:
         # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
-        is_gzipped, is_valid = check_gzip( dataset.path )
+        is_gzipped, is_valid, is_bam = check_gzip( dataset.path )
         if is_gzipped and not is_valid:
             file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
             return
-        elif is_gzipped and is_valid:
-            # We need to uncompress the temp_name file
+        elif is_gzipped and is_valid and is_bam:
+            ext = 'bam'
+            data_type = 'bam'
+        elif is_gzipped and is_valid and not is_bam:
+            # We need to uncompress the temp_name file, but BAM files must remain compressed
+            # in order for samtools to function on them
             CHUNK_SIZE = 2**20 # 1Mb   
-            fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ) )
-            gzipped_file = gzip.GzipFile( dataset.path )
+            fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False )
+            gzipped_file = gzip.GzipFile( dataset.path, 'rb' )
             while 1:
                 try:
                     chunk = gzipped_file.read( CHUNK_SIZE )
@@ -229,7 +248,7 @@ def add_file( dataset, json_file, output_path ):
             if check_html( dataset.path ):
                 file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
                 return
-        if data_type != 'binary' and data_type != 'zip':
+        if data_type != 'bam' and data_type != 'binary' and data_type != 'zip':
             if dataset.space_to_tab:
                 line_count = sniff.convert_newlines_sep2tabs( dataset.path )
             else:

tools/samtools/sam_to_bam.py

@@ -1,31 +1,27 @@
 #! /usr/bin/python
-
 """
-Converts SAM data to BAM format.
-
-usage: %prog [options]
-   -i, --input1=i: SAM file to be converted
-   -d, --dbkey=d: dbkey value
-   -r, --ref_file=r: Reference file if choosing from history
-   -o, --output1=o: BAM output
-   -x, --index_dir=x: Index directory
-
-usage: %prog input_file dbkey ref_list output_file
+Converts SAM data to sorted BAM data.
+usage: sam_to_bam.py [options]
+   --input1: SAM file to be converted
+   --dbkey: dbkey value
+   --ref_file: Reference file if choosing from history
+   --output1: output dataset in bam format
+   --index_dir: GALAXY_DATA_INDEX_DIR
 """
 
-import os, sys, tempfile
+import optparse, os, sys, subprocess, tempfile, shutil, gzip
 from galaxy import eggs
 import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.cookbook import doc_optparse
+from galaxy import util
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
     sys.exit()
 
-def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
-    seq_file = "%s/sam_fa_indices.loc" % GALAXY_DATA_INDEX_DIR
+def check_seq_file( dbkey, cached_seqs_pointer_file ):
     seq_path = ''
-    for line in open( seq_file ):
+    for line in open( cached_seqs_pointer_file ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( "#" ) and line.startswith( 'index' ):
             fields = line.split( '\t' )
@@ -38,48 +34,80 @@ def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
  
 def __main__():
     #Parse Command Line
-    options, args = doc_optparse.parse( __doc__ )
-    seq_path = check_seq_file( options.dbkey, options.index_dir )
+    parser = optparse.OptionParser()
+    parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
+    parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' )
+    parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
+    parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
+    parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
+    ( options, args ) = parser.parse_args()
+
+    cached_seqs_pointer_file = "%s/sam_fa_indices.loc" % options.index_dir
+    if not os.path.exists( cached_seqs_pointer_file ):
+        stop_err( "The required file (%s) does not exist." % cached_seqs_pointer_file )
+    # If found for the dbkey, seq_path will look something like /depot/data2/galaxy/equCab2/sam_index/equCab2.fa,
+    # and the equCab2.fa file will contain fasta sequences.
+    seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file )
     tmp_dir = tempfile.gettempdir()
-    os.chdir(tmp_dir)
-    tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir)
-    tmpf1fai = '%s.fai' % tmpf1.name
-    tmpf2 = tempfile.NamedTemporaryFile(dir=tmp_dir)
-    tmpf3 = tempfile.NamedTemporaryFile(dir=tmp_dir)
-    tmpf3bam = '%s.bam' % tmpf3.name
     if options.ref_file == "None":
-        full_path = "%s.fai" % seq_path 
-        if not os.path.exists( full_path ):
-            stop_err( "No sequences are available for '%s', request them by reporting this error." % options.dbkey )
-        cmd1 = "cp %s %s; cp %s %s" % (seq_path, tmpf1.name, full_path, tmpf1fai)
+        # We're using locally cached reference sequences( e.g., /depot/data2/galaxy/equCab2/sam_index/equCab2.fa ).
+        # The indexes for /depot/data2/galaxy/equCab2/sam_index/equCab2.fa will be contained in
+        # a file named /depot/data2/galaxy/equCab2/sam_index/equCab2.fa.fai
+        fai_index_file_path = "%s.fai" % seq_path 
+        if not os.path.exists( fai_index_file_path ):
+            stop_err( "No sequences are available for build (%s), request them by reporting this error." % options.dbkey )
     else:
-        cmd1 = "cp %s %s; samtools faidx %s 2>/dev/null" % (options.ref_file, tmpf1.name, tmpf1.name) 
-    cmd2 = "samtools view -bt %s -o %s %s 2>/dev/null" % (tmpf1fai, tmpf2.name, options.input1)   
-    cmd3 = "samtools sort %s %s 2>/dev/null" % (tmpf2.name, tmpf3.name)
-    cmd4 = "cp %s %s" % (tmpf3bam, options.output1)
-    # either create index based on fa file or copy provided index to temp directory 
+        try:
+            # Create indexes for history reference ( e.g., ~/database/files/000/dataset_1.dat ) using samtools faidx, which will:
+            # - index reference sequence in the FASTA format or extract subsequence from indexed reference sequence
+            # - if no region is specified, faidx will index the file and create <ref.fasta>.fai on the disk
+            # - if regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format
+            # - the input file can be compressed in the RAZF format.
+            # IMPORTANT NOTE: a real weakness here is that we are creating indexes for the history dataset
+            # every time we run this tool.  It would be nice if we could somehow keep track of user's specific
+            # index files so they could be re-used.
+            fai_index_file_path = os.path.join( tmp_dir, os.path.basename( options.ref_file ) )
+            # At this point, fai_index_file_path will look something like /tmp/dataset_13.dat
+            os.symlink( options.ref_file, fai_index_file_path )
+            command = "samtools faidx %s 2>/dev/null" % fai_index_file_path
+            proc = subprocess.Popen( args=command, shell=True )
+            proc.wait()
+        except Exception, e:
+            stop_err( 'Error creating indexes from reference (%s), %s' % ( options.ref_file, str( e ) ) )
     try:
-        os.system(cmd1)
-    except Exception, eq:
-        stop_err("Error creating the reference list index.\n" + str(eq))
-    # create original bam file
+        # Extract all alignments from the input SAM file to BAM format ( since no region is specified, all the alignments will be extracted ).
+        tmp_aligns_file = tempfile.NamedTemporaryFile()
+        tmp_aligns_file_name = tmp_aligns_file.name
+        tmp_aligns_file.close()
+        # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning,
+        # and the docs do not currently state that this occurs ( very bad ).
+        command = "samtools view -bt %s -o %s %s 2>/dev/null" % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) 
+        proc = subprocess.Popen( args=command, shell=True )
+        proc.wait()
+    except Exception, e:
+        stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
     try:
-        os.system(cmd2)
-    except Exception, eq:
-        stop_err("Error running view command.\n" + str(eq))
-    # sort original bam file to produce sorted output bam file
-    try:
-        os.system(cmd3)
-        os.system(cmd4)
-    except Exception, eq:
-        stop_err("Error sorting data and creating output file.\n" + str(eq))
-    # cleanup temp files
-    tmpf1.close()
-    tmpf2.close()
-    tmpf3.close()
-    if os.path.exists(tmpf1fai):
-        os.remove(tmpf1fai)
-    if os.path.exists(tmpf3bam):
-        os.remove(tmpf3bam)
+        # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
+        # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
+        # into memory ( controlled by option -m ).
+        tmp_sorted_aligns_file = tempfile.NamedTemporaryFile()
+        tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name
+        tmp_sorted_aligns_file.close()
+        command = "samtools sort %s %s 2>/dev/null" % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name )
+        proc = subprocess.Popen( args=command, shell=True )
+        proc.wait()
+    except Exception, e:
+        stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) )
+    # Move tmp_aligns_file_name to our output dataset location
+    sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name
+    shutil.move( sorted_bam_file, options.output1 )
+    if options.ref_file != "None":
+        # Remove the symlink from /tmp/dataset_13.dat to ~/database/files/000/dataset_13.dat
+        os.unlink( fai_index_file_path )
+        # Remove the index file
+        index_file_name = '%s.fai' % fai_index_file_path
+        os.unlink( index_file_name )
+    # Remove the tmp_aligns_file_name
+    os.unlink( tmp_aligns_file_name )
 
 if __name__=="__main__": __main__()

tools/samtools/sam_to_bam.xml

@@ -1,32 +1,29 @@
 <tool id="sam_to_bam" name="SAM-to-BAM" version="1.0.0">
   <description>converts SAM format to BAM format</description>
   <command interpreter="python">
-    sam_to_bam.py 
-        --input1=$source.input1
-        --dbkey=${input1.metadata.dbkey} 
-        #if $source.indexSource == "history":
-         --ref_file=$ref_file
-        #else
-         --ref_file="None"
-        #end if
-        --output1=$output1
-        --index_dir=${GALAXY_DATA_INDEX_DIR}
+sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} 
+#if $source.index_source == "history":
+--ref_file=$source.ref_file
+#else
+--ref_file="None"
+#end if
+--output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR}
   </command>
   <inputs>
     <conditional name="source">
-      <param name="indexSource" type="select" label="Choose the source for the reference list">
-        <option value="built_in">Built-in</option>
+      <param name="index_source" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
         <option value="history">History</option>
       </param>
-      <when value="built_in">
+      <when value="cached">
         <param name="input1" type="data" format="sam" label="SAM File to Convert">
            <validator type="unspecified_build" />
            <validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
         </param>
       </when>
       <when value="history">
-        <param name="input1" type="data" format="sam" label="SAM File to Convert" />
-        <param name="ref_file" type="data" format="fasta" label="Choose the reference file" />
+        <param name="input1" type="data" format="sam" label="Convert SAM file" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
       </when>
     </conditional>
   </inputs>
@@ -34,19 +31,16 @@
     <data name="output1" format="bam"/>
   </outputs>
   <tests>
+    <!--
+    # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning,
+    # and the docs do not currently state that this occurs ( very bad ).
+    -->
     <test>
-      <param name="indexSource" value="history" /> 
-      <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" />
-      <param name="ref_file" value="chrM.fa" ftype="fasta" />
+      <param name="index_source" value="history" /> 
+      <param name="input1" value="3.sam" ftype="sam" />
+      <param name="ref_file" value="chr_m.fasta" ftype="fasta" />
       <output name="output1" file="sam_to_bam_out1.bam" />
     </test>
-<!--  chrM is not a built-in dbkey (in the builds.txt list) so can't be tested
-    <test>
-      <param name="indexSource" value="built_in" />
-      <param name="input1" value="sam_to_bam_in2.sam" ftype="sam" dbkey="chrM" />
-      <output name="output1" file="sam_to_bam_out2.bam" />
-    </test>
--->
   </tests>
   <help>
 

tools/sr_mapping/bowtie_wrapper.xml

@@ -338,7 +338,7 @@
     </test>
     <test>
       <param name="genomeSource" value="history" />
-      <param name="ownFile" value="chrM.fa" />
+      <param name="ownFile" value="chr_m.fasta" />
       <param name="index_settings" value="index_pre_set" />
       <param name="sPaired" value="paired" />
       <param name="input1" ftype="fastqsanger" value="bowtie_in2.fastq" />
@@ -349,7 +349,7 @@
     </test>
     <test>
       <param name="genomeSource" value="history" />
-      <param name="ownFile" value="chrM.fa" />
+      <param name="ownFile" value="chr_m.fasta" />
       <param name="index_settings" value="index_full" />
       <param name="auto_b" value="set" />
       <param name="packed" value="unpacked" />

tools/sr_mapping/lastz_wrapper.xml

@@ -125,10 +125,13 @@
         <requirement type="binary">lastz</requirement>
     </requirements>
     <tests>
-        <test> <!-- Lastz command: lastz phiX.2bit/PHIX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam 
-        			You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data 
-        			You will have to replace all the pluses before the commands with 2 dashes, 
-        			as double-dash can't appear in an XML comment -->
+        <test>
+            <!--
+            Lastz command:
+            lastz phiX.2bit/PHIX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam 
+            You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data.  You will have to replace all the pluses before the
+            commands with 2 dashes, as double-dash can't appear in an XML comment.
+            -->
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="cached" />
             <param name="input1_2bit" value="phiX" />
@@ -156,10 +159,13 @@
             <param name="num_threads" value="4" />
             <output name="output1" file="lastz_wrapper_out2.sam" />
         </test>
-        <test> <!-- Lastz command: lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular 
-        			phiX.fasta and b1.fasta are located in galaxy's test-data 
-        			You will have to replace all the pluses before the commands with 2 dashes, 
-        			as double-dash can't appear in an XML comment -->
+        <test>
+            <!--
+            Lastz command:
+            lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular 
+        	phiX.fasta and b1.fasta are located in galaxy's test-data.  You will have to replace all the pluses before the commands with 2 dashes, 
+            as double-dash can't appear in an XML comment.
+            -->
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="history" />
             <param name="input1" value="phiX.fasta" ftype="fasta" />
@@ -173,14 +179,7 @@
             <param name="num_threads" value="4" />
             <output name="output1" file="lastz_wrapper_out3.tabular" />
         </test>
-        <test> <!-- Lastz command: first you will need to split the file phiX_split.fasta into two files, 
-        			phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
-        			lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular 
-        			lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular 
-        			You need to point to phiX1.fasta and phiX2.fasta somewhere on your system. 
-        			phiX_split.fasta and b1.fasta are located in galaxy's test-data 
-        			You will have to replace all the asterisks before the commands with 2 dashes, 
-        			as double-dash can't appear in an XML comment -->
+        <test>
             <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="history" />
             <param name="input1" value="phiX_split.fasta" ftype="fasta"  />