# HG changeset patch
# User devteam
# Date 1580991071 0
# Node ID 37df866ccf1af18848cff332abcf6a12f8dc6dd0
# Parent efd77ef84903e4e3a839e722300089656e894a1d
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_pileup commit 8301d37348be25a038b3c63b049b1178d05f5003"
diff -r efd77ef84903 -r 37df866ccf1a sam_pileup.py
--- a/sam_pileup.py Tue Oct 13 12:30:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Creates a pileup file from a bam file and a reference.
-
-usage: %prog [options]
- -p, --input1=p: bam file
- -o, --output1=o: Output pileup
- -R, --ref=R: Reference file type
- -n, --ownFile=n: User-supplied fasta reference file
- -b, --bamIndex=b: BAM index file
- -g, --index=g: Path of the indexed reference genome
- -s, --lastCol=s: Print the mapping quality as the last column
- -i, --indels=i: Only output lines containing indels
- -M, --mapCap=M: Cap mapping quality
- -c, --consensus=c: Call the consensus sequence using MAQ consensu model
- -T, --theta=T: Theta paramter (error dependency coefficient)
- -N, --hapNum=N: Number of haplotypes in sample
- -r, --fraction=r: Expected fraction of differences between a pair of haplotypes
- -I, --phredProb=I: Phred probability of an indel in sequencing/prep
-
-"""
-
-import os, shutil, subprocess, sys, tempfile
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.cookbook import doc_optparse
-
-def stop_err( msg ):
- sys.stderr.write( '%s\n' % msg )
- sys.exit()
-
-def __main__():
- #Parse Command Line
- options, args = doc_optparse.parse( __doc__ )
- # output version # of tool
- try:
- tmp = tempfile.NamedTemporaryFile().name
- tmp_stdout = open( tmp, 'wb' )
- proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
- tmp_stdout.close()
- returncode = proc.wait()
- stdout = None
- for line in open( tmp_stdout.name, 'rb' ):
- if line.lower().find( 'version' ) >= 0:
- stdout = line.strip()
- break
- if stdout:
- sys.stdout.write( 'Samtools %s\n' % stdout )
- else:
- raise Exception
- except:
- sys.stdout.write( 'Could not determine Samtools version\n' )
- #prepare file names
- tmpDir = tempfile.mkdtemp()
- tmpf0 = tempfile.NamedTemporaryFile( dir=tmpDir )
- tmpf0_name = tmpf0.name
- tmpf0.close()
- tmpf0bam_name = '%s.bam' % tmpf0_name
- tmpf0bambai_name = '%s.bam.bai' % tmpf0_name
- tmpf1 = tempfile.NamedTemporaryFile( dir=tmpDir )
- tmpf1_name = tmpf1.name
- tmpf1.close()
- #link bam and bam index to working directory (can't move because need to leave original)
- os.symlink( options.input1, tmpf0bam_name )
- os.symlink( options.bamIndex, tmpf0bambai_name )
- #get parameters for pileup command
- if options.lastCol == 'yes':
- lastCol = '-s'
- else:
- lastCol = ''
- if options.indels == 'yes':
- indels = '-i'
- else:
- indels = ''
- opts = '%s %s -M %s' % ( lastCol, indels, options.mapCap )
- if options.consensus == 'yes':
- opts += ' -c -T %s -N %s -r %s -I %s' % ( options.theta, options.hapNum, options.fraction, options.phredProb )
- #prepare basic pileup command
- cmd = 'samtools pileup %s -f %s %s > %s'
- try:
- # have to nest try-except in try-finally to handle 2.4
- try:
- #index reference if necessary and prepare pileup command
- if options.ref == 'indexed':
- if not os.path.exists( "%s.fai" % options.index ):
- raise Exception, "Indexed genome %s not present, request it by reporting this error." % options.index
- cmd = cmd % ( opts, options.index, tmpf0bam_name, options.output1 )
- elif options.ref == 'history':
- os.symlink( options.ownFile, tmpf1_name )
- cmdIndex = 'samtools faidx %s' % ( tmpf1_name )
- tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, 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()
- #did index succeed?
- if returncode != 0:
- raise Exception, 'Error creating index file\n' + stderr
- cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 )
- #perform pileup command
- tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name
- tmp_stderr = open( tmp, 'wb' )
- proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() )
- returncode = proc.wait()
- tmp_stderr.close()
- #did it succeed?
- # 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()
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
- stop_err( 'Error running Samtools pileup tool\n' + str( e ) )
- finally:
- #clean up temp files
- if os.path.exists( tmpDir ):
- shutil.rmtree( tmpDir )
- # check that there are results in the output file
- if os.path.getsize( options.output1 ) > 0:
- sys.stdout.write( 'Converted BAM to pileup' )
- else:
- stop_err( 'The output file is empty. Your input file may have had no matches, or there may be an error with your input file or settings.' )
-
-if __name__ == "__main__" : __main__()
diff -r efd77ef84903 -r 37df866ccf1a sam_pileup.xml
--- a/sam_pileup.xml Tue Oct 13 12:30:34 2015 -0400
+++ b/sam_pileup.xml Thu Feb 06 12:11:11 2020 +0000
@@ -1,124 +1,126 @@
-
- from BAM dataset
-
- samtools
-
-
- sam_pileup.py
- --input1=$input1
- --output=$output1
- --ref=$refOrHistory.reference
- #if $refOrHistory.reference == "history":
- --ownFile=$refOrHistory.ownFile
- #else:
- --index=${refOrHistory.index.fields.path}
- #end if
- --bamIndex=${input1.metadata.bam_index}
- --lastCol=$lastCol
- --indels=$indels
- --mapCap=$mapCap
- --consensus=$c.consensus
- #if $c.consensus == "yes":
- --theta=$c.theta
- --hapNum=$c.hapNum
- --fraction=$c.fraction
- --phredProb=$c.phredProb
- #else:
- --theta="None"
- --hapNum="None"
- --fraction="None"
- --phredProb="None"
- #end if
-
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+ from BAM dataset
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+ samtools
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+ '$output1'
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+ 10.1093/bioinformatics/btp352
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diff -r efd77ef84903 -r 37df866ccf1a tool_dependencies.xml
--- a/tool_dependencies.xml Tue Oct 13 12:30:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
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