Mercurial > repos > galaxyp > ms_data_converter
comparison ms_data_converter.xml @ 1:a36e9f847308 default tip
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 |
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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 --> |