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comparison ms_data_converter.xml @ 1:a36e9f847308 default tip

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Fixes for running on Windows via pulsar
author Jim Johnson <jj@umn.edu>
date Wed, 11 Mar 2015 16:47:12 -0500
parents dfafbfd7983d
children
comparison
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0:dfafbfd7983d 1:a36e9f847308
16 #if hasattr($input, 'display_name') 16 #if hasattr($input, 'display_name')
17 #set basename = $re.sub('\W','_',$input.display_name) 17 #set basename = $re.sub('\W','_',$input.display_name)
18 #end if 18 #end if
19 --input="${input.extra_files_path}/wiff" 19 --input="${input.extra_files_path}/wiff"
20 --input_name="${basename}.wiff" 20 --input_name="${basename}.wiff"
21 #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_scan')): 21 #### The os.path.exist did not work on Windows
22 ## #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_scan')):
22 --implicit="${input.extra_files_path}/wiff_scan" 23 --implicit="${input.extra_files_path}/wiff_scan"
23 --input="${input.extra_files_path}/wiff_scan" 24 --input="${input.extra_files_path}/wiff_scan"
24 --input_name="${basename}.wiff.scan" 25 --input_name="${basename}.wiff.scan"
25 #end if 26 ## #end if
26 #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_mtd')): 27 #### The os.path.exist did not work on Windows
28 ## #if $os.path.exists($os.path.join($input.extra_files_path,'wiff_mtd')):
27 --implicit="${input.extra_files_path}/wiff_mtd" 29 --implicit="${input.extra_files_path}/wiff_mtd"
28 --input="${input.extra_files_path}/wiff_mtd" 30 --input="${input.extra_files_path}/wiff_mtd"
29 --input_name="${basename}.wiff.mtd" 31 --input_name="${basename}.wiff.mtd"
30 #end if 32 ## #end if
31 --output=${output} 33 --output=${output}
32 ## BEGIN_VERSION_DEFAULT 34 ## BEGIN_VERSION_DEFAULT
33 --fromextension=$ext 35 --fromextension=$ext
34 --content_type=$content_type 36 --content_type=$content_type
35 ## END_VERSION_DEFAULT 37 ## END_VERSION_DEFAULT
37 #if $result.output_format == "mzML" 39 #if $result.output_format == "mzML"
38 --zlib=${result.zlib} 40 --zlib=${result.zlib}
39 --binaryencoding=${result.precision} 41 --binaryencoding=${result.precision}
40 --index=${result.index} 42 --index=${result.index}
41 #end if 43 #end if
44 --debug
42 </command> 45 </command>
43 46
44 <inputs> 47 <inputs>
45 48
46 <!-- BEGIN_VERSION_DEFAULT --> 49 <!-- BEGIN_VERSION_DEFAULT -->