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comparison msconvert_macros.xml @ 11:cc5ccfa8ee28 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d
author galaxyp
date Thu, 28 Feb 2019 14:14:44 -0500
parents 9d5de24e6ef7
children 9b61227976d6
comparison
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10:9d5de24e6ef7 11:cc5ccfa8ee28
7 <![CDATA[ 7 <![CDATA[
8 #import re 8 #import re
9 #set $ext = $input.ext 9 #set $ext = $input.ext
10 10
11 ## sanitize display name for use as temp filename 11 ## sanitize display name for use as temp filename
12 #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier) 12 #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
13 13
14 #if $ext == 'wiff': 14 #if $ext == 'wiff':
15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' && 15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' && 16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
17 #set inputmask = "'"+$basename+"'"
17 #elif $ext.endswith('tar'): 18 #elif $ext.endswith('tar'):
18 ln -s '$input' '${basename}' && 19 ln -s '$input' '${basename}' &&
19 tar xf '${basename}' && 20 tar xf '${basename}' &&
20 #set basename = $os.path.splitext($basename)[0] 21 #set basename = $os.path.splitext($basename)[0]
22 #if $ext.startswith('waters'):
23 #set inputmask = '*.raw'
24 #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
25 #set inputmask = '*.d'
26 #elif $ext.startswith('wiff'):
27 #set inputmask = '*.wiff *.wiff2'
28 #else
29 #raise RuntimeError("Unrecognized type of tar (${ext})")
30 #end if
21 #else 31 #else
22 ln -s '$input' '${basename}' && 32 ln -s '$input' '${basename}' &&
33 #set inputmask = "'"+$basename+"'"
23 #end if 34 #end if
24 35
25 #if $data_processing.precursor_refinement.use_mzrefinement 36 #if $data_processing.precursor_refinement.use_mzrefinement
26 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) 37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
27 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' 38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
28 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && 39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
29 #end if 40 #end if
30 41
31 uid=`id -u` && 42 uid=`id -u` &&
32 gid=`id -g` && 43 gid=`id -g` &&
33 44
34 wine64_anyuser msconvert '${basename}' 45 wine64_anyuser msconvert ${inputmask}
35 --outdir outputs 46 --outdir outputs
36 --${output_type} 47 --${output_type}
37 48
38 #if $general_options.combineIonMobilitySpectra: 49 #if $general_options.combineIonMobilitySpectra:
39 --combineIonMobilitySpectra 50 --combineIonMobilitySpectra