# HG changeset patch
# User devteam
# Date 1493924381 14400
# Node ID bdd9fcdb398ebee95a86766ab31236e8150a0e7f
# Parent  9326d6e6882a18cb8f52927c986f89436d41e30e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 397bc85634156862fdaa3d74b8f1e53752876619

diff -r 9326d6e6882a -r bdd9fcdb398e bowtie_wrapper.py
--- a/bowtie_wrapper.py	Sun Jan 08 08:00:56 2017 -0500
+++ b/bowtie_wrapper.py	Thu May 04 14:59:41 2017 -0400
@@ -64,19 +64,24 @@
     --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is'
 """
 
-import optparse, os, shutil, subprocess, sys, tempfile
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
 
-#Allow more than Sanger encoded variants
+# Allow more than Sanger encoded variants
 DEFAULT_ASCII_ENCODING = '--phred33-quals'
-GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = { 'fastqsanger':'--phred33-quals', 'fastqillumina':'--phred64-quals', 'fastqsolexa':'--solexa-quals' }
-#FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
+GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG = {'fastqsanger': '--phred33-quals', 'fastqillumina': '--phred64-quals', 'fastqsolexa': '--solexa-quals'}
+# FIXME: Integer quality scores are supported only when the '--integer-quals' argument is specified to bowtie; this is not currently able to be set in the tool/wrapper/config
+
 
 def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
+    sys.exit('%s\n' % msg)
+
 
 def __main__():
-    #Parse Command Line
     parser = optparse.OptionParser()
     parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' )
     parser.add_option( '-o', '--output', dest='output', help='The output file' )
@@ -152,7 +157,7 @@
     # index if necessary
     if options.genomeSource == 'history' and not options.do_not_build_index:
         # set up commands
-        if options.index_settings =='indexPreSet':
+        if options.index_settings == 'indexPreSet':
             indexing_cmds = '%s' % colorspace
         else:
             try:
@@ -204,7 +209,7 @@
                                 ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc,
                                   inoref, options.ioffrate, iftab, intoa, iendian,
                                   iseed, colorspace )
-            except ValueError, e:
+            except ValueError as e:
                 # clean up temp dir
                 if os.path.exists( tmp_index_dir ):
                     shutil.rmtree( tmp_index_dir )
@@ -216,25 +221,22 @@
         cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name )
         try:
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
-            # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
-            stderr = ''
-            buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
+            with open(tmp, 'w') as tmp_stderr:
+                returncode = subprocess.call(args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
             if returncode != 0:
-                raise Exception, stderr
-        except Exception, e:
+                # get stderr, allowing for case where it's very large
+                stderr = ''
+                buffsize = 1048576
+                with open(tmp, 'r') as tmp_stderr:
+                    try:
+                        while True:
+                            stderr += tmp_stderr.read(buffsize)
+                            if not stderr or len(stderr) % buffsize != 0:
+                                break
+                    except OverflowError:
+                        pass
+                raise Exception(stderr)
+        except Exception as e:
             # clean up temp dir
             if os.path.exists( tmp_index_dir ):
                 shutil.rmtree( tmp_index_dir )
@@ -261,7 +263,7 @@
     quality_score_encoding = GALAXY_FORMAT_TO_QUALITY_SCORE_ENCODING_ARG.get( options.galaxy_input_format, DEFAULT_ASCII_ENCODING )
     if options.params == 'preSet':
         aligning_cmds = '-q %s %s -p %s -S %s %s %s ' % \
-                ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
+            ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace, quality_score_encoding )
     else:
         try:
             if options.skip and int( options.skip ) > 0:
@@ -280,13 +282,13 @@
                 trimL = '-3 %s' % options.trimL
             else:
                 trimL = ''
-            if options.maxMismatches and (options.maxMismatches == '0' or options.maxMismatches == '1' \
-                        or options.maxMismatches == '2' or options.maxMismatches == '3'):
+            if options.maxMismatches and (options.maxMismatches == '0' or options.maxMismatches == '1' or
+                                          options.maxMismatches == '2' or options.maxMismatches == '3'):
                 maxMismatches = '-v %s' % options.maxMismatches
             else:
                 maxMismatches = ''
-            if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \
-                        or options.mismatchSeed == '2' or options.mismatchSeed == '3'):
+            if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' or
+                                         options.mismatchSeed == '2' or options.mismatchSeed == '3'):
                 mismatchSeed = '-n %s' % options.mismatchSeed
             else:
                 mismatchSeed = ''
@@ -400,7 +402,7 @@
                               strata, offrate, seed, snpphred, snpfrac, keepends,
                               output_unmapped_reads, output_suppressed_reads,
                               quality_score_encoding )
-        except ValueError, e:
+        except ValueError as e:
             # clean up temp dir
             if os.path.exists( tmp_index_dir ):
                 shutil.rmtree( tmp_index_dir )
@@ -415,51 +417,48 @@
                 cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
             # align
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
-            tmp_stderr = open( tmp, 'wb' )
-            proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stdout=sys.stdout, stderr=tmp_stderr.fileno() )
-            returncode = proc.wait()
-            tmp_stderr.close()
+            with open(tmp, 'w') as tmp_stderr:
+                returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
             # get stderr, allowing for case where it's very large
-            tmp_stderr = open( tmp, 'rb' )
             stderr = ''
             buffsize = 1048576
-            try:
-                while True:
-                    stderr += tmp_stderr.read( buffsize )
-                    if not stderr or len( stderr ) % buffsize != 0:
-                        break
-            except OverflowError:
-                pass
-            tmp_stderr.close()
+            with open(tmp, 'r') as tmp_stderr:
+                try:
+                    while True:
+                        stderr += tmp_stderr.read(buffsize)
+                        if not stderr or len(stderr) % buffsize != 0:
+                            break
+                except OverflowError:
+                    pass
             if returncode != 0:
-                raise Exception, stderr
+                raise Exception(stderr)
             elif options.output_mapping_stats is not None:
                 # Write stderr (containing the mapping statistics) to a named file
                 with open(options.output_mapping_stats, 'w') as mapping_stats:
                     mapping_stats.write( stderr )
             # get suppressed and unmapped reads output files in place if appropriate
             if options.paired == 'paired' and tmp_suppressed_file_name and \
-                               options.output_suppressed_reads_l and options.output_suppressed_reads_r:
+                    options.output_suppressed_reads_l and options.output_suppressed_reads_r:
                 try:
                     left = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
                     right = tmp_suppressed_file_name.replace( '.fastq', '_1.fastq' )
                     shutil.move( left, options.output_suppressed_reads_l )
                     shutil.move( right, options.output_suppressed_reads_r )
-                except Exception, e:
+                except Exception as e:
                     sys.stdout.write( 'Error producing the suppressed output file.\n' )
             if options.paired == 'paired' and tmp_unmapped_file_name and \
-                               options.output_unmapped_reads_l and options.output_unmapped_reads_r:
+                    options.output_unmapped_reads_l and options.output_unmapped_reads_r:
                 try:
                     left = tmp_unmapped_file_name.replace( '.fastq', '_1.fastq' )
                     right = tmp_unmapped_file_name.replace( '.fastq', '_2.fastq' )
                     shutil.move( left, options.output_unmapped_reads_l )
                     shutil.move( right, options.output_unmapped_reads_r )
-                except Exception, e:
+                except Exception as e:
                     sys.stdout.write( 'Error producing the unmapped output file.\n' )
             # check that there are results in the output file
             if os.path.getsize( options.output ) == 0:
-                raise Exception, 'The output file is empty, there may be an error with your input file or settings.'
-        except Exception, e:
+                raise Exception('The output file is empty, there may be an error with your input file or settings.')
+        except Exception as e:
             stop_err( 'Error aligning sequence. ' + str( e ) )
     finally:
         # clean up temp dir
@@ -468,5 +467,6 @@
     stdout += 'Sequence file aligned.\n'
     sys.stdout.write( stdout )
 
+
 if __name__ == "__main__":
     __main__()
diff -r 9326d6e6882a -r bdd9fcdb398e bowtie_wrapper.xml
--- a/bowtie_wrapper.xml	Sun Jan 08 08:00:56 2017 -0500
+++ b/bowtie_wrapper.xml	Thu May 04 14:59:41 2017 -0400
@@ -1,8 +1,8 @@
 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.2.0">
+  <description></description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
   </requirements>
-  <description></description>
   <version_command>bowtie --version</version_command>
   <command>
     python '$__tool_directory__/bowtie_wrapper.py'
@@ -167,7 +167,7 @@
         </param>
       </when>
       <when value="history">
-        <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
+        <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
         <conditional name="indexParams">
           <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
             <option value="indexPreSet">Default</option>
@@ -313,7 +313,7 @@
       <when value="paired">
         <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
         <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
-            <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
+            <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
                <column name="name" index="0"/>
                <column name="value" index="0"/>
                <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>