changeset 0:1d373f219445 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:22:05 -0400
parents
children
files fastqc/README fastqc/fastqc.py fastqc/fastqc.xml
diffstat 3 files changed, 300 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+
+FastQC
+------
+
+From the FastQC website   http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
+
+Function	A quality control tool for high throughput sequence data.
+Language	Java
+Requirements	A suitable Java Runtime Environment 
+		The Picard BAM/SAM Libraries (included in download)
+Code Maturity	Stable. Mature code, but feedback is appreciated.
+Code Released	Yes, under GPL v3 or later.
+Initial Contact	Simon Andrews
+
+FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
+
+The main functions of FastQC are:
+
+- Import of data from BAM, SAM or FastQ files (any variant)
+- Providing a quick overview to tell you in which areas there may be problems
+- Summary graphs and tables to quickly assess your data
+- Export of results to an HTML based permanent report
+- Offline operation to allow automated generation of reports without running the interactive application
+
+Download and installation information is at: http://www.bioinformatics.bbsrc.ac.uk/projects/download.html#fastqc
+
+
+Galaxy Tool Wrapper
+-------------------
+
+The galaxy tool wrapper for FastQC requires version:   FastQC v0.7.2 
+
+FastQC should be downloaded and installed on the system on which it will be executed.  
+The PATH environment variable should include the directory in which the fastqc script resides.
+
+The fastqc.py wrapper invokes the fastqc script provided in FastQC download, 
+and converts the FastQC results into a Galaxy html formatted dataset.
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc/fastqc.py	Tue Jun 07 17:22:05 2011 -0400
@@ -0,0 +1,167 @@
+#!/usr/bin/env python
+
+"""
+Runs FastQC on a fastq file;
+TODO: more documentation
+
+usage: fastqc.py [options]
+    -i, --input=i: The fastq input file
+    -n, --name=n: The fastq input name
+    -c, --contaminants=c: A contaminants file
+    -r, --report=r: The html summary report file
+    -D, --dir=D: The dir for report files
+    -d, --data=d: The data output text file
+"""
+
+import optparse, os, shutil, subprocess, sys, tempfile, re, string
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-i', '--input', dest='input', help='The sequence input file' )
+    parser.add_option( '-f', '--format', dest='format', help='The sequence input file format' )
+    parser.add_option( '-n', '--name', dest='name', help='The fastq input name' )
+    parser.add_option( '-c', '--contaminants', dest='contaminants', help='A contaminants file' )
+    parser.add_option( '-r', '--report', dest='report', help='The HTML report' )
+    parser.add_option( '-D', '--dir', dest='outdir', help='The dir for report files' )
+    parser.add_option( '-d', '--data', dest='data', help='The output data text file' )
+    (options, args) = parser.parse_args()
+    if options.input == None:
+       stop_err("Misssing option --input")
+    params = []
+    #params.append('-Xmx250m')
+    params.append('-Djava.awt.headless=true')
+    name = 'input'
+    format = 'fastq'
+    if options.outdir != None:
+        os.makedirs(options.outdir)
+    if options.contaminants != None and options.contaminants != 'None':
+        params.append("-c %s" % options.contaminants)
+    if options.name != None and options.name != 'None':
+       name = re.sub('[^a-zA-Z0-9_.-]','_',options.name)
+    if options.format != None and options.format != 'None':
+        format = options.format
+        params.append("-f %s" % options.format)
+    # FastQC relies on the extension to determine file format .sam .bam or .fastq
+    if not name.endswith('.'+format):
+        name = '.'.join((name,format))
+    # make temp directory
+    buffsize = 1048576
+    tmp_dir = tempfile.mkdtemp()
+    params.append("-o %s" % tmp_dir)
+    # print("tmp_dir %s" % tmp_dir)
+    try:
+        # make a link to the input fastq in the tmp_dir
+        # FastQC will generate output in the same dir that it finds its input
+        fastq = os.path.join(tmp_dir,name) 
+        os.symlink( options.input, fastq)
+        # generate commandline
+        cmd = 'fastqc %s %s' % (' '.join(params),fastq)
+        # need to nest try-except in try-finally to handle 2.4
+        try:
+            try:
+                tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
+                tmp_stderr = open( tmp_stderr_name, 'wb' )
+                tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name
+                tmp_stdout = open( tmp_stdout_name, 'wb' )
+                proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
+                returncode = proc.wait()
+                tmp_stderr.close()
+                # get stderr, allowing for case where it's very large
+                tmp_stderr = open( tmp_stderr_name, 'rb' )
+                stderr = ''
+                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:
+                raise Exception, 'Error executing FastQC. ' + str( e )
+            # remove the input file symlink so it does get copied
+            os.remove(fastq)
+            # remove the stdout and stderr files so they do not get copied
+            os.remove(tmp_stderr_name)
+            os.remove(tmp_stdout_name)
+            # array to retrieve results of each test so that it gets displayed in the tool info 
+            tests = []
+            # move result to outdir 
+            # Need to flatten the dir hierachy in order for galaxy to serve the href links
+            for root, dirs, files in os.walk(tmp_dir):
+                for fname in files:
+                    path = os.path.join(root,fname)
+                    # print("%s" % fname)
+                    if re.match('.+\.zip',fname):
+                        pass
+                    elif fname == 'fastqc_report.html':
+                        if options.outdir != None:
+                            fsrc = open(path,'r')
+                            # fdst = open(os.path.join(options.outdir,fname),'w')
+                            fdst = open(options.report,'w')
+                            try:
+                                for line in fsrc:
+                                    if line.find('footer') > 0:
+                                        # add extra links in case someone prefers raw text
+                                        fdst.write('<p><a href="summary.txt">FastQC Summary text report</a>')
+                                        fdst.write('<p><a href="fastqc_data.txt">FastQC Report Data</a>')
+                                    # copy lines removing subdirs from links
+                                    fdst.write(re.sub('Icons/|Images/','',line))
+                            finally:
+                                fsrc.close()
+                                fdst.close() 
+                    else:
+                        if options.outdir != None:
+                            shutil.copy(path,options.outdir)
+                        if fname == 'summary.txt':
+                            # Use the contents of this file to put stdout info into the HistoryDataset panel
+                            fsrc = open(path,'r')
+                            try:
+                                for line in fsrc:
+                                    (grade,test,seq) = string.split(line,'	')
+                                    tests.append("%s %s" % ('+' if grade == 'PASS' else '-',re.sub('equence','eq',test)))
+                            finally:
+                                fsrc.close()
+                        elif fname == 'fastqc_data.txt':
+                            if options.data != None:
+                                # copy the fastqc_data.txt file to the dataset data 
+                                shutil.copy(path,options.data)
+                            cnt = '?'
+                            flen = '?'
+                            gc = '?'
+                            fsrc = open(path,'r')
+                            try:
+                                for line in fsrc:
+                                    m = re.match('^Total Sequences	(\d+)',line)
+                                    if m:
+                                        cnt = m.groups()[-1]
+                                    m =  re.match('^Sequence length	(\d+)',line)
+                                    if m:
+                                        flen = m.groups()[-1]
+                                    m = re.match('^%GC	(\d+)',line)
+                                    if m:
+                                        gc = m.groups()[-1]
+                            finally:
+                                fsrc.close()
+                            #print to stdout so that this appears in the tool dataset info
+                            print("Seqs %s, Len %s, GC %s" %(cnt,flen,gc)) 
+            #print to stdout so that this appears in the tool dataset info
+            print("%s" % '\n'.join(tests))
+        except Exception, e:
+            stop_err( 'Fastq failed.\n' + str( e ) )
+    finally:
+        # clean up temp dir, put in a try block so we don't fail on stale nfs handles
+        try: 
+            if os.path.exists( tmp_dir ):
+                shutil.rmtree( tmp_dir )
+        except Exception, e:
+            pass
+
+if __name__=="__main__": __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc/fastqc.xml	Tue Jun 07 17:22:05 2011 -0400
@@ -0,0 +1,94 @@
+<tool id="FastQC" name="FastQC" version="1.0.0">
+  <description>quality control checks on raw sequence data</description>
+  <command interpreter="python">fastqc.py
+   #if $input.extension.startswith( "fastq"):
+    --format=fastq
+   #else
+    --format=$input.extension
+   #end if
+   --input='$input'
+   --name='$input.name'
+   --dir='$report.extra_files_path'
+   --report='$report'
+   #if $contaminants != None and $contaminants != "None" and $contaminants != "":
+     --contaminants=$contaminants 
+   #end if
+  </command>
+  <inputs>
+   <param name="input" type="data" format="fastq,sam,bam" label="FASTQ reads" />
+   <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminants" 
+           help="Two fields per line separated by a TAB: name DNA_sequence.  For example: Illumina Small RNA RT Primer	CAAGCAGAAGACGGCATACGA"/>
+  </inputs>
+  <outputs>
+    <data name="report" format="html" />
+  </outputs>
+  <tests>
+    <!--
+    <test>
+      <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
+      <output name="output1_file" file="split_pair_reads_1.fastqsanger" />
+      <output name="output2_file" file="split_pair_reads_2.fastqsanger" />
+    </test>
+    -->
+  </tests>
+  <help>
+**What it does**
+
+FastQC_ is a product of Bioinformatics Group at the Babraham Institute.  FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
+
+The main functions of FastQC are::
+
+  - Import of data from BAM, SAM or FastQ files (any variant)
+  - Provding a quick overview to tell you in which areas there may be problems
+  - Summary graphs and tables to quickly assess your data
+  - Export of results to an HTML based permanent report
+  - Offline operation to allow automated generation of reports without running the interactive application
+
+
+.. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
+
+-----
+
+**Input format**
+
+Any fastq file, for example::
+
+    @HWI-EAS91_1_30788AAXX:7:21:1542:1758
+    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
+    +HWI-EAS91_1_30788AAXX:7:21:1542:1758
+    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
+
+**Contaminants format**
+
+An optional contaminant file (otherwise FastQC will use the default)::
+
+  # This file contains a list of potential contaminants which are
+  # frequently found in high throughput sequencing reactions.  These
+  # are mostly sequences of adapters / primers used in the various
+  # sequencing chemistries.
+  # 
+  # You can add more sequences to the file by putting one line per entry
+  # and specifying a name[tab]sequence.  If the contaminant you add is 
+  # likely to be of use to others please consider sending it to the FastQ
+  # authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
+  # or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
+  # the program can benefit.
+  Illumina Single End Apapter 1   ACACTCTTTCCCTACACGACGCTGTTCCATCT
+  Illumina Single End Apapter 2   CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+  Illumina Single End PCR Primer 1        AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+  Illumina Single End PCR Primer 2        CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+  Illumina Single End Sequencing Primer   ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+
+-----
+
+**Outputs**
+
+An HTML file with links to::
+
+  - fastqc_report.html
+  - summary.txt
+  - fastqc_data.txt
+
+  </help>
+</tool>