commit/galaxy-central: 2 new changesets

19 Jan 2013

2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/0df1612c1cb1/
changeset:   0df1612c1cb1
user:        asbardellati
date:        2013-01-18 17:11:04
summary:     Add option for writing not aligned reads to file

Reviewed-by: Nicola Soranzo <soranzo@crs4.it>
affected #:  2 files

diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r 0df1612c1cb14b48f5bee405a04886de5380df39 tools/sr_mapping/bowtie2_wrapper.py

--- a/tools/sr_mapping/bowtie2_wrapper.py
+++ b/tools/sr_mapping/bowtie2_wrapper.py
@@ -31,10 +31,29 @@
     parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' )
     parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
 
+    parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' )
+    parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' )
+    parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' )
+
     (options, args) = parser.parse_args()
     
+    tmp_unaligned_file_name = None
     # Creat bowtie index if necessary.
     tmp_index_dir = tempfile.mkdtemp()
+    
+    if options.single_paired == 'paired':
+        if options.output_unaligned_reads_l and options.output_unaligned_reads_r:
+            tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
+            tmp_unaligned_file_name = tmp_unaligned_file.name
+            tmp_unaligned_file.close()
+            output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name
+        else:
+            output_unaligned_reads = ''
+    elif options.output_unaligned_reads:
+        output_unaligned_reads = '--un %s' % options.output_unaligned_reads
+    else:
+        output_unaligned_reads = ''
+    
     if options.own_file:
         index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) )
         try:
@@ -71,7 +90,7 @@
         index_path = options.index_path
 
     # Build bowtie command; use view and sort to create sorted bam.
-    cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s'
+    cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s'
     
     # Set up reads.
     if options.single_paired == 'paired':
@@ -104,7 +123,7 @@
         opts += ' --rg %s:%s' % ( 'SM', options.rgsm )
         
     # Final command:
-    cmd = cmd % ( opts, index_path, reads, options.output )
+    cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output )
     print cmd
 
     # Run
@@ -136,6 +155,16 @@
     except Exception, e:
         stop_err( 'Error in bowtie2:\n' + str( e ) ) 
 
+    # get unaligned reads output files in place if appropriate
+    if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r:
+        try:
+            left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' )
+            right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' )
+            shutil.move( left, options.output_unaligned_reads_l )
+            shutil.move( right, options.output_unaligned_reads_r )
+        except Exception, e:
+            sys.stdout.write( 'Error producing the unaligned output files.\n' )
+
     # Clean up temp dirs
     if os.path.exists( tmp_index_dir ):
         shutil.rmtree( tmp_index_dir )

diff -r b9d44cf4b68e2c4a76bc2b7f7eb54950e2c077be -r 0df1612c1cb14b48f5bee405a04886de5380df39 tools/sr_mapping/bowtie2_wrapper.xml
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -1,6 +1,6 @@
 <tool id="bowtie2" name="Bowtie2" version="0.1"><!-- Wrapper compatible with Bowtie version 2.0.0 -->
-    <description>is a short-read mapper</description>
+    <description>is a short-read aligner</description><version_command>bowtie2 --version</version_command><requirements><requirement type="package">bowtie2</requirement>
@@ -15,6 +15,17 @@
         ## Outputs.
         --output=$output
 
+        #if str( $singlePaired.sPaired ) == "single"
+            #if $output_unaligned_reads_l
+                --output_unaligned_reads=$output_unaligned_reads_l
+            #end if
+        #else
+            #if $output_unaligned_reads_l and $output_unaligned_reads_r
+                --output_unaligned_reads_l=$output_unaligned_reads_l
+                --output_unaligned_reads_r=$output_unaligned_reads_r
+            #end if
+        #end if
+        
         ## Handle reference file.
         #if $refGenomeSource.genomeSource == "history":
             --own-file=$refGenomeSource.ownFile
@@ -71,6 +82,7 @@
                 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional>
+        <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and  --un-conc for paired-ends)" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option>
@@ -133,7 +145,7 @@
     </inputs><outputs>
-        <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+        <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed">
@@ -152,6 +164,22 @@
             </conditional></actions></data>
+        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
+            <filter>unalignedFile is True</filter>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="singlePaired.input1" param_attribute="ext" />
+                </action>
+            </actions>
+        </data>
+        <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
+            <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="singlePaired.input1" param_attribute="ext" />
+                </action>
+            </actions>
+        </data></outputs><tests>


https://bitbucket.org/galaxy/galaxy-central/commits/7d37ffe813f2/
changeset:   7d37ffe813f2
user:        jgoecks
date:        2013-01-19 22:35:28
summary:     Merged in nsoranzo/galaxy-central (pull request #110)

Add option to bowtie2 tool for writing not aligned reads to file
affected #:  2 files

diff -r 50c65739cd1af36f48672a980db378783dffcdd5 -r 7d37ffe813f2a037b560af26770ffe5924ae643f tools/sr_mapping/bowtie2_wrapper.py
--- a/tools/sr_mapping/bowtie2_wrapper.py
+++ b/tools/sr_mapping/bowtie2_wrapper.py
@@ -31,10 +31,29 @@
     parser.add_option( '', '--rgpl', dest='rgpl', help='Platform/technology used to produce the reads' )
     parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' )
 
+    parser.add_option( '', '--output_unaligned_reads', dest='output_unaligned_reads', help='File name for unaligned reads (single-end)' )
+    parser.add_option( '', '--output_unaligned_reads_l', dest='output_unaligned_reads_l', help='File name for unaligned reads (left, paired-end)' )
+    parser.add_option( '', '--output_unaligned_reads_r', dest='output_unaligned_reads_r', help='File name for unaligned reads (right, paired-end)' )
+
     (options, args) = parser.parse_args()
     
+    tmp_unaligned_file_name = None
     # Creat bowtie index if necessary.
     tmp_index_dir = tempfile.mkdtemp()
+    
+    if options.single_paired == 'paired':
+        if options.output_unaligned_reads_l and options.output_unaligned_reads_r:
+            tmp_unaligned_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir, suffix='.fastq' )
+            tmp_unaligned_file_name = tmp_unaligned_file.name
+            tmp_unaligned_file.close()
+            output_unaligned_reads = '--un-conc %s' % tmp_unaligned_file_name
+        else:
+            output_unaligned_reads = ''
+    elif options.output_unaligned_reads:
+        output_unaligned_reads = '--un %s' % options.output_unaligned_reads
+    else:
+        output_unaligned_reads = ''
+    
     if options.own_file:
         index_path = os.path.join( tmp_index_dir, '.'.join( os.path.split( options.own_file )[1].split( '.' )[:-1] ) )
         try:
@@ -71,7 +90,7 @@
         index_path = options.index_path
 
     # Build bowtie command; use view and sort to create sorted bam.
-    cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s'
+    cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s'
     
     # Set up reads.
     if options.single_paired == 'paired':
@@ -104,7 +123,7 @@
         opts += ' --rg %s:%s' % ( 'SM', options.rgsm )
         
     # Final command:
-    cmd = cmd % ( opts, index_path, reads, options.output )
+    cmd = cmd % ( opts, index_path, reads, output_unaligned_reads, options.output )
     print cmd
 
     # Run
@@ -136,6 +155,16 @@
     except Exception, e:
         stop_err( 'Error in bowtie2:\n' + str( e ) ) 
 
+    # get unaligned reads output files in place if appropriate
+    if options.single_paired == 'paired' and tmp_unaligned_file_name and options.output_unaligned_reads_l and options.output_unaligned_reads_r:
+        try:
+            left = tmp_unaligned_file_name.replace( '.fastq', '.1.fastq' )
+            right = tmp_unaligned_file_name.replace( '.fastq', '.2.fastq' )
+            shutil.move( left, options.output_unaligned_reads_l )
+            shutil.move( right, options.output_unaligned_reads_r )
+        except Exception, e:
+            sys.stdout.write( 'Error producing the unaligned output files.\n' )
+
     # Clean up temp dirs
     if os.path.exists( tmp_index_dir ):
         shutil.rmtree( tmp_index_dir )

diff -r 50c65739cd1af36f48672a980db378783dffcdd5 -r 7d37ffe813f2a037b560af26770ffe5924ae643f tools/sr_mapping/bowtie2_wrapper.xml
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -1,6 +1,6 @@
 <tool id="bowtie2" name="Bowtie2" version="0.1"><!-- Wrapper compatible with Bowtie version 2.0.0 -->
-    <description>is a short-read mapper</description>
+    <description>is a short-read aligner</description><version_command>bowtie2 --version</version_command><requirements><requirement type="package">bowtie2</requirement>
@@ -15,6 +15,17 @@
         ## Outputs.
         --output=$output
 
+        #if str( $singlePaired.sPaired ) == "single"
+            #if $output_unaligned_reads_l
+                --output_unaligned_reads=$output_unaligned_reads_l
+            #end if
+        #else
+            #if $output_unaligned_reads_l and $output_unaligned_reads_r
+                --output_unaligned_reads_l=$output_unaligned_reads_l
+                --output_unaligned_reads_r=$output_unaligned_reads_r
+            #end if
+        #end if
+        
         ## Handle reference file.
         #if $refGenomeSource.genomeSource == "history":
             --own-file=$refGenomeSource.ownFile
@@ -71,6 +82,7 @@
                 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /></when></conditional>
+        <param name="unalignedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (uses --un for single-end and  --un-conc for paired-ends)" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option>
@@ -133,7 +145,7 @@
     </inputs><outputs>
-        <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+        <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads"><actions><conditional name="refGenomeSource.genomeSource"><when value="indexed">
@@ -152,6 +164,22 @@
             </conditional></actions></data>
+        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
+            <filter>unalignedFile is True</filter>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="singlePaired.input1" param_attribute="ext" />
+                </action>
+            </actions>
+        </data>
+        <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
+            <filter>singlePaired['sPaired'] == "paired" and unalignedFile is True</filter>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="singlePaired.input1" param_attribute="ext" />
+                </action>
+            </actions>
+        </data></outputs><tests>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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