Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.py @ 11:570228bb2fb7 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 53544cd620f81c5cfbdcb277e835f1c6da8588b0
author pjbriggs
date Mon, 18 Jun 2018 07:27:33 -0400
parents b47cf1d6fb47
children fb2af52d67d1
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b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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1 #!/usr/bin/env python
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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2 #
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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3 # Wrapper script to run Amplicon_analysis_pipeline.sh
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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4 # from Galaxy tool
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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5
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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6 import sys
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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7 import os
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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8 import argparse
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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9 import subprocess
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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10 import glob
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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11
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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12 class PipelineCmd(object):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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13 def __init__(self,cmd):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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14 self.cmd = [str(cmd)]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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15 def add_args(self,*args):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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16 for arg in args:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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17 self.cmd.append(str(arg))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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18 def __repr__(self):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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19 return ' '.join([str(arg) for arg in self.cmd])
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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20
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21 def ahref(target,name=None,type=None):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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22 if name is None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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23 name = os.path.basename(target)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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24 ahref = "<a href='%s'" % target
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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25 if type is not None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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26 ahref += " type='%s'" % type
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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27 ahref += ">%s</a>" % name
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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28 return ahref
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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29
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30 def check_errors():
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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31 # Errors in Amplicon_analysis_pipeline.log
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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32 with open('Amplicon_analysis_pipeline.log','r') as pipeline_log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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33 log = pipeline_log.read()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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34 if "Names in the first column of Metatable.txt and in the second column of Final_name.txt do not match" in log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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35 print_error("""*** Sample IDs don't match dataset names ***
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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36
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37 The sample IDs (first column of the Metatable file) don't match the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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38 supplied sample names for the input Fastq pairs.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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39 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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40 # Errors in pipeline output
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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41 with open('pipeline.log','r') as pipeline_log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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42 log = pipeline_log.read()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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43 if "Errors and/or warnings detected in mapping file" in log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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44 with open("Metatable_log/Metatable.log","r") as metatable_log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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45 # Echo the Metatable log file to the tool log
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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46 print_error("""*** Error in Metatable mapping file ***
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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47
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48 %s""" % metatable_log.read())
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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49 elif "No header line was found in mapping file" in log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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50 # Report error to the tool log
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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51 print_error("""*** No header in Metatable mapping file ***
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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52
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53 Check you've specified the correct file as the input Metatable""")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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54
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55 def print_error(message):
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56 width = max([len(line) for line in message.split('\n')]) + 4
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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57 sys.stderr.write("\n%s\n" % ('*'*width))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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58 for line in message.split('\n'):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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59 sys.stderr.write("* %s%s *\n" % (line,' '*(width-len(line)-4)))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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60 sys.stderr.write("%s\n\n" % ('*'*width))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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61
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62 def clean_up_name(sample):
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63 # Remove trailing "_L[0-9]+_001" from Fastq
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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64 # pair names
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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65 split_name = sample.split('_')
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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66 if split_name[-1] == "001":
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67 split_name = split_name[:-1]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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68 if split_name[-1].startswith('L'):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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69 try:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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70 int(split_name[-1][1:])
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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71 split_name = split_name[:-1]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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72 except ValueError:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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73 pass
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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74 return '_'.join(split_name)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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75
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76 def list_outputs(filen=None):
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77 # List the output directory contents
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78 # If filen is specified then will be the filename to
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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79 # write to, otherwise write to stdout
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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80 if filen is not None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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81 fp = open(filen,'w')
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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82 else:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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83 fp = sys.stdout
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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84 results_dir = os.path.abspath("RESULTS")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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85 fp.write("Listing contents of output dir %s:\n" % results_dir)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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86 ix = 0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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87 for d,dirs,files in os.walk(results_dir):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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88 ix += 1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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89 fp.write("-- %d: %s\n" % (ix,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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90 os.path.relpath(d,results_dir)))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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91 for f in files:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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92 ix += 1
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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93 fp.write("---- %d: %s\n" % (ix,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
94 os.path.relpath(f,results_dir)))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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95 # Close output file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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96 if filen is not None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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97 fp.close()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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98
8
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diff changeset
99 def find_executable(name):
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
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100 # Locate executable on PATH
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
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101 for p in os.environ['PATH'].split(os.pathsep):
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
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102 exe = os.path.join(name)
9
32a43bc3dd58 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
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103 if os.path.isfile(exe) and os.access(exe,os.X_OK):
8
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
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104 return exe
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
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diff changeset
105 return None
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
106
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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107 if __name__ == "__main__":
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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108 # Command line
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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109 print "Amplicon analysis: starting"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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110 p = argparse.ArgumentParser()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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111 p.add_argument("metatable",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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112 metavar="METATABLE_FILE",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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113 help="Metatable.txt file")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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114 p.add_argument("fastq_pairs",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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115 metavar="SAMPLE_NAME FQ_R1 FQ_R2",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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116 nargs="+",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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117 default=list(),
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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118 help="Triplets of SAMPLE_NAME followed by "
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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119 "a R1/R2 FASTQ file pair")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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120 p.add_argument("-g",dest="forward_pcr_primer")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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121 p.add_argument("-G",dest="reverse_pcr_primer")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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122 p.add_argument("-q",dest="trimming_threshold")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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123 p.add_argument("-O",dest="minimum_overlap")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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124 p.add_argument("-L",dest="minimum_length")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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125 p.add_argument("-l",dest="sliding_window_length")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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126 p.add_argument("-P",dest="pipeline",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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127 choices=["vsearch","uparse","qiime"],
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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128 type=str.lower,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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129 default="vsearch")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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130 p.add_argument("-S",dest="use_silva",action="store_true")
2
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131 p.add_argument("-H",dest="use_homd",action="store_true")
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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132 p.add_argument("-r",dest="reference_data_path")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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133 p.add_argument("-c",dest="categories_file")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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134 args = p.parse_args()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
135
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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136 # Build the environment for running the pipeline
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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137 print "Amplicon analysis: building the environment"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
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138 metatable_file = os.path.abspath(args.metatable)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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139 os.symlink(metatable_file,"Metatable.txt")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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140 print "-- made symlink to Metatable.txt"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
141
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
142 # Link to Categories.txt file (if provided)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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143 if args.categories_file is not None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
144 categories_file = os.path.abspath(args.categories_file)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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145 os.symlink(categories_file,"Categories.txt")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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146 print "-- made symlink to Categories.txt"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
147
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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148 # Link to FASTQs and construct Final_name.txt file
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diff changeset
149 sample_names = []
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
150 with open("Final_name.txt",'w') as final_name:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
151 fastqs = iter(args.fastq_pairs)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
152 for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
153 sample_name = clean_up_name(sample_name)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
154 r1 = "%s_R1_.fastq" % sample_name
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
155 r2 = "%s_R2_.fastq" % sample_name
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
156 os.symlink(fqr1,r1)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
157 os.symlink(fqr2,r2)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
158 final_name.write("%s\n" % '\t'.join((r1,sample_name)))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
159 final_name.write("%s\n" % '\t'.join((r2,sample_name)))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
160 sample_names.append(sample_name)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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diff changeset
161
2
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parents: 0
diff changeset
162 # Reference database
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diff changeset
163 if args.use_silva:
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diff changeset
164 ref_database = "silva"
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diff changeset
165 elif args.use_homd:
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diff changeset
166 ref_database = "homd"
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diff changeset
167 else:
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diff changeset
168 ref_database = "gg"
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diff changeset
169
8
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pjbriggs
parents: 2
diff changeset
170 # Executables
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pjbriggs
parents: 2
diff changeset
171 os.mkdir("bin")
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
172 os.environ["PATH"] = os.path.abspath("bin") + \
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
173 os.pathsep + \
10
b47cf1d6fb47 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
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diff changeset
174 os.environ["PATH"]
8
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
175 print "-- updated PATH: %s" % os.environ["PATH"]
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
176 # Pipeline wants 'vsearch113' but bioconda version is just
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
177 # 'vsearch'
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pjbriggs
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diff changeset
178 vsearch = find_executable("vsearch113")
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
179 if vsearch is None:
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
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diff changeset
180 vsearch = find_executable("vsearch")
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
181 if vsearch:
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
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diff changeset
182 os.symlink(vsearch,os.path.join("bin","vsearch113"))
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
183 print "-- made symlink to %s" % vsearch
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
184 else:
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
185 sys.stderr.write("Missing 'vsearch[113]'\n")
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
186 # Pipeline wants 'fasta-splitter.pl' but bioconda provides
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
187 # 'fasta-splitter'
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pjbriggs
parents: 2
diff changeset
188 fasta_splitter = find_executable("fasta-splitter.pl")
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
parents: 2
diff changeset
189 if fasta_splitter is None:
11
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pjbriggs
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diff changeset
190 fasta_splitter = os.readlink(
8
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
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diff changeset
191 find_executable("fasta-splitter"))
8292f8262a9d planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty
pjbriggs
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192 if fasta_splitter:
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193 os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
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diff changeset
194 else:
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pjbriggs
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195 sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")
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pjbriggs
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diff changeset
196
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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197 # Construct the pipeline command
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198 print "Amplicon analysis: constructing pipeline command"
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pjbriggs
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199 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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200 if args.forward_pcr_primer:
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pjbriggs
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201 pipeline.add_args("-g",args.forward_pcr_primer)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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202 if args.reverse_pcr_primer:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
203 pipeline.add_args("-G",args.reverse_pcr_primer)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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204 if args.trimming_threshold:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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205 pipeline.add_args("-q",args.trimming_threshold)
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pjbriggs
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206 if args.minimum_overlap:
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pjbriggs
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207 pipeline.add_args("-O",args.minimum_overlap)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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208 if args.minimum_length:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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209 pipeline.add_args("-L",args.minimum_length)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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210 if args.sliding_window_length:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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211 pipeline.add_args("-l",args.sliding_window_length)
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pjbriggs
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212 if args.reference_data_path:
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pjbriggs
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213 pipeline.add_args("-r",args.reference_data_path)
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pjbriggs
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214 pipeline.add_args("-P",args.pipeline)
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215 if ref_database == "silva":
0
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216 pipeline.add_args("-S")
2
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217 elif ref_database == "homd":
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218 pipeline.add_args("-H")
0
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219
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pjbriggs
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220 # Echo the pipeline command to stdout
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221 print "Running %s" % pipeline
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pjbriggs
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222
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pjbriggs
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223 # Run the pipeline
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224 with open("pipeline.log","w") as pipeline_out:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
225 try:
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pjbriggs
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226 subprocess.check_call(pipeline.cmd,
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pjbriggs
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227 stdout=pipeline_out,
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228 stderr=subprocess.STDOUT)
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229 exit_code = 0
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230 print "Pipeline completed ok"
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231 except subprocess.CalledProcessError as ex:
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232 # Non-zero exit status
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233 sys.stderr.write("Pipeline failed: exit code %s\n" %
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diff changeset
234 ex.returncode)
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235 exit_code = ex.returncode
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pjbriggs
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diff changeset
236 except Exception as ex:
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237 # Some other problem
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238 sys.stderr.write("Unexpected error: %s\n" % str(ex))
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diff changeset
239 exit_code = 1
0
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240
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241 # Write out the list of outputs
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242 outputs_file = "Pipeline_outputs.txt"
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pjbriggs
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243 list_outputs(outputs_file)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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244
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245 # Check for log file
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pjbriggs
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246 log_file = "Amplicon_analysis_pipeline.log"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
247 if os.path.exists(log_file):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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248 print "Found log file: %s" % log_file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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249 if exit_code == 0:
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pjbriggs
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250 # Create an HTML file to link to log files etc
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pjbriggs
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251 # NB the paths to the files should be correct once
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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252 # copied by Galaxy on job completion
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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253 with open("pipeline_outputs.html","w") as html_out:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
254 html_out.write("""<html>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
255 <head>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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256 <title>Amplicon analysis pipeline: log files</title>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
257 <head>
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diff changeset
258 <body>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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diff changeset
259 <h1>Amplicon analysis pipeline: log files</h1>
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pjbriggs
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diff changeset
260 <ul>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
261 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
262 html_out.write(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
263 "<li>%s</li>\n" %
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
264 ahref("Amplicon_analysis_pipeline.log",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
265 type="text/plain"))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
266 html_out.write(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
267 "<li>%s</li>\n" %
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
268 ahref("pipeline.log",type="text/plain"))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
269 html_out.write(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
270 "<li>%s</li>\n" %
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
271 ahref("Pipeline_outputs.txt",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
272 type="text/plain"))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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diff changeset
273 html_out.write(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
274 "<li>%s</li>\n" %
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
275 ahref("Metatable.html"))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
276 html_out.write("""<ul>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
277 </body>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
278 </html>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
279 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
280 else:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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281 # Check for known error messages
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
282 check_errors()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
283 # Write pipeline stdout to tool stderr
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
284 sys.stderr.write("\nOutput from pipeline:\n")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
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diff changeset
285 with open("pipeline.log",'r') as log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
286 sys.stderr.write("%s" % log.read())
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
287 # Write log file contents to tool log
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
288 print "\nAmplicon_analysis_pipeline.log:"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
289 with open(log_file,'r') as log:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
290 print "%s" % log.read()
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
291 else:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
292 sys.stderr.write("ERROR missing log file \"%s\"\n" %
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
293 log_file)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
294
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
295 # Handle FastQC boxplots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
296 print "Amplicon analysis: collating per base quality boxplots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
297 with open("fastqc_quality_boxplots.html","w") as quality_boxplots:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
298 # PHRED value for trimming
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
299 phred_score = 20
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
300 if args.trimming_threshold is not None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
301 phred_score = args.trimming_threshold
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
302 # Write header for HTML output file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
303 quality_boxplots.write("""<html>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
304 <head>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
305 <title>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</title>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
306 <head>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
307 <body>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
308 <h1>Amplicon analysis pipeline: Per-base Quality Boxplots (FastQC)</h1>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
309 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
310 # Look for raw and trimmed FastQC output for each sample
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
311 for sample_name in sample_names:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
312 fastqc_dir = os.path.join(sample_name,"FastQC")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
313 quality_boxplots.write("<h2>%s</h2>" % sample_name)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
314 for d in ("Raw","cutdapt_sickle/Q%s" % phred_score):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
315 quality_boxplots.write("<h3>%s</h3>" % d)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
316 fastqc_html_files = glob.glob(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
317 os.path.join(fastqc_dir,d,"*_fastqc.html"))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
318 if not fastqc_html_files:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
319 quality_boxplots.write("<p>No FastQC outputs found</p>")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
320 continue
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
321 # Pull out the per-base quality boxplots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
322 for f in fastqc_html_files:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
323 boxplot = None
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
324 with open(f) as fp:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
325 for line in fp.read().split(">"):
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
326 try:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
327 line.index("alt=\"Per base quality graph\"")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
328 boxplot = line + ">"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
329 break
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
330 except ValueError:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
331 pass
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
332 if boxplot is None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
333 boxplot = "Missing plot"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
334 quality_boxplots.write("<h4>%s</h4><p>%s</p>" %
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
335 (os.path.basename(f),
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
336 boxplot))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
337 quality_boxplots.write("""</body>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
338 </html>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
339 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
340
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
341 # Handle additional output when categories file was supplied
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
342 if args.categories_file is not None:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
343 # Alpha diversity boxplots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
344 print "Amplicon analysis: indexing alpha diversity boxplots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
345 boxplots_dir = os.path.abspath(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
346 os.path.join("RESULTS",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
347 "%s_%s" % (args.pipeline.title(),
2
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
348 ref_database),
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
349 "Alpha_diversity",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
350 "Alpha_diversity_boxplot",
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
351 "Categories_shannon"))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
352 print "Amplicon analysis: gathering PDFs from %s" % boxplots_dir
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
353 boxplot_pdfs = [os.path.basename(pdf)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
354 for pdf in
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
355 sorted(glob.glob(
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
356 os.path.join(boxplots_dir,"*.pdf")))]
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
357 with open("alpha_diversity_boxplots.html","w") as boxplots_out:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
358 boxplots_out.write("""<html>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
359 <head>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
360 <title>Amplicon analysis pipeline: Alpha Diversity Boxplots (Shannon)</title>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
361 <head>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
362 <body>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
363 <h1>Amplicon analysis pipeline: Alpha Diversity Boxplots (Shannon)</h1>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
364 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
365 boxplots_out.write("<ul>\n")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
366 for pdf in boxplot_pdfs:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
367 boxplots_out.write("<li>%s</li>\n" % ahref(pdf))
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
368 boxplots_out.write("<ul>\n")
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
369 boxplots_out.write("""</body>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
370 </html>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
371 """)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
372
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
373 # Finish
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
374 print "Amplicon analysis: finishing, exit code: %s" % exit_code
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
375 sys.exit(exit_code)