msconvert: msconvert_macros.xml annotate

annotate msconvert_macros.xml @ 9:a13a1ee66232 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d

author	galaxyp
date	Fri, 22 Mar 2019 14:16:55 -0400
parents	dff86cbe69f2
children	06747cba5685

rev	line source
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	1 <macros>
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	2 <token name="@VERSION@">3.0.19052</token>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	3 <token name="@FULL_VERSION@">@VERSION@-089e81090</token>
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	4
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	5 <xml name="msconvertCommand">
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	6 <command detect_errors="exit_code">
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	7 <![CDATA[
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	8 #import re
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	9 #set $ext = $input.ext
5 637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea galaxyp parents: 4 diff changeset	10
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	11 ## sanitize display name for use as temp filename
8 dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	12 #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	13
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	14 #if $ext == 'wiff':
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
8 dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	17 #set inputmask = "'"+$basename+"'"
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	18 #elif $ext.endswith('tar'):
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	19 ln -s '$input' '${basename}' &&
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	20 tar xf '${basename}' &&
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	21 #set basename = $os.path.splitext($basename)[0]
8 dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	22 #if $ext.startswith('waters'):
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	23 #set inputmask = '*.raw'
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	24 #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	25 #set inputmask = '*.d'
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	26 #elif $ext.startswith('wiff'):
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	27 #set inputmask = '.wiff .wiff2'
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	28 #else
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	29 #raise RuntimeError("Unrecognized type of tar (${ext})")
dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	30 #end if
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	31 #else
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	32 ln -s '$input' '${basename}' &&
8 dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	33 #set inputmask = "'"+$basename+"'"
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	34 #end if
8 dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	35
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	36 #if $data_processing.precursor_refinement.use_mzrefinement
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	40 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	41
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	42 uid=`id -u` &&
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	43 gid=`id -g` &&
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	44
8 dff86cbe69f2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 3c189141a9dd1d44d44af82ccd9b6e9d3742f93d galaxyp parents: 7 diff changeset	45 wine64_anyuser msconvert ${inputmask}
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	46 --outdir outputs
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	47 --${output_type}
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	48
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	49 #if $general_options.combineIonMobilitySpectra:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	50 --combineIonMobilitySpectra
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	51 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	52
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	53 #if $general_options.simAsSpectra:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	54 --simAsSpectra
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	55 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	56
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	57 #if $general_options.srmAsSpectra:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	58 --srmAsSpectra
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	59 #end if
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	60
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	61 #if $general_options.acceptZeroLengthSpectra:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	62 --acceptZeroLengthSpectra
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	63 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	64
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	65 #if $general_options.ignoreUnknownInstrumentError:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	66 --ignoreUnknownInstrumentError
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	67 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	68
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	69 #if $general_options.scan_summing.do_scan_summing:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	70 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	71 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	72
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	73 #if $general_options.multi_run_output.do_multi_run_output:
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	74 #if len($general_options.multi_run_output.run_index_set) > 0
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	75 --runIndexSet "
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	76 #for $index in $general_options.multi_run_output.run_index_set
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	77 [${index.from},${index.to}]
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	78 #end for
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	79 "
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	80 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	81 #else
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	82 --runIndexSet $general_options.multi_run_output.runIndexSet
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	83 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	84
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	85 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	86 --stripLocationFromSourceFiles
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	87
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	88 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	89 #if $data_processing.peak_picking.pick_peaks
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	90 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	91 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	92
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	93 #if $data_processing.precursor_refinement.use_mzrefinement
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	94 --filter "mzRefiner $input_ident_name
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	95 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	96 thresholdScore=$data_processing.precursor_refinement.thresholdScore
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	97 thresholdValue=$data_processing.precursor_refinement.thresholdValue
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	98 thresholdStep=$data_processing.precursor_refinement.thresholdStep
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	99 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	100 #end if
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	101
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	102 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	103 --filter "chargeStatePredictor
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	104 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	105 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	106 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	107 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	108 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	109 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	110 --filter "turbocharger
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	111 minCharge=$data_processing.charge_state_calculation.minCharge
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	112 maxCharge=$data_processing.charge_state_calculation.maxCharge
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	113 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	114 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	115 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	116 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	117 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	118 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	119
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	120 #for threshold_entry in $data_processing.thresholds
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	121 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	122 #end for
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	123
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	124 #if $data_processing.filter_mz_windows.do_mzwindow_filter
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	125 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	126 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	127
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	128 #if $data_processing.etd_filtering.do_etd_filtering
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	129 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	130 $data_processing.etd_filtering.remove_charge_reduced
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	131 $data_processing.etd_filtering.remove_neutral_loss
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	132 $data_processing.etd_filtering.blanket_removal
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	133 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	134 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	135
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	136 #if $data_processing.ms2denoise.denoise
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	137 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	138 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	139
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	140 #if str($data_processing.ms2deisotope) == "true"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	141 --filter "MS2Deisotope"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	142 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	143
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	144
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	145 ## SCAN INCLUSION/EXCLUSION FILTERS
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	146 #if str($filtering.activation) != "false"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	147 --filter "activation $filtering.activation"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	148 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	149
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	150 #if len($filtering.indices) > 0
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	151 --filter "index
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	152 #for $index in $filtering.indices
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	153 [${index.from},${index.to}]
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	154 #end for
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	155 "
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	156 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	157
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	158 #if len($filtering.scan_numbers) > 0
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	159 --filter "scanNumber
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	160 #for $scan_number in $filtering.scan_numbers
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	161 [${scan_number.from},${scan_number.to}]
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	162 #end for
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	163 "
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	164 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	165
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	166 #if $filtering.strip_it.value
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	167 --filter "stripIT"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	168 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	169
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	170 #if $filtering.filter_ms_levels.do_ms_level_filter
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	171 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	172 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	173
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	174 #if str($filtering.polarity) != "false"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	175 --filter "polarity $filtering.polarity"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	176 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	177
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	178 #if str($filtering.analyzer) != "false"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	179 --filter "analyzer $filtering.analyzer"
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	180 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	181
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	182 ## OUTPUT ENCODING
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	183 #set $mz_encoding = str($settings.mz_encoding)
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	184 #set $intensity_encoding = str($settings.intensity_encoding)
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	185 #if $mz_encoding == $intensity_encoding
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	186 #if $mz_encoding == "64"
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	187 --64
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	188 #else
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	189 --32
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	190 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	191 #else
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	192 --mz${mz_encoding}
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	193 --inten${intensity_encoding}
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	194 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	195
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	196 #set binary_compression = str($settings.binary_compression)
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	197 #if $binary_compression == "zlib"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	198 --zlib
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	199 #else if $binary_compression == "numpressLinearPic"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	200 --numpressLinear --numpressPic
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	201 #else if $binary_compression == "numpressLinearSlof"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	202 --numpressLinear --numpressSlof
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	203 #else if $binary_compression == "numpressLinear"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	204 --numpressLinear
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	205 #else if $binary_compression == "numpressPic"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	206 --numpressPic
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	207 #else if $binary_compression == "numpressSlof"
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	208 --numpressSlof
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	209 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	210
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	211 #if $settings.gzip_compression
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	212 --gzip
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	213 #end if
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	214
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	215 #if $general_options.multi_run_output.do_multi_run_output == 'false':
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	216 --outfile '${os.path.splitext($basename)[0]}'
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	217 && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}'
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	218 #else
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	219 && sudo chown \$uid:\$gid 'outputs' -R
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	220 && ls -la outputs/
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	221 #end if
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	222
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	223 #if $data_processing.precursor_refinement.use_mzrefinement
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	224 && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement'
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	225 #end if
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	226 ]]>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	227 </command>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	228 </xml>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	229
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	230 <xml name="msconvertInputParameters">
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	231 <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses proprietary vendor libraries; to run it you must agree to the vendor licenses. Read them at http://www.proteowizard.org/licenses.html">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	232 <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	233 </param>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	234
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	235 <param name="output_type" type="select" label="Output Type">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	236 <option value="mz5" selected="true">mz5</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	237 <option value="mzML">mzML</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	238 <option value="mzXML">mzXML</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	239 <option value="mgf">mgf</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	240 <option value="ms2">ms2</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	241 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	242
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	243 <section name="data_processing" title="Data Processing Filters">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	244 <conditional name="peak_picking">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	245 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	246 <when value="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	247 <when value="true">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	248 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	249 <option value="1">MS1 Only (1)</option>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	250 <option value="2">MS2 Only (2)</option>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	251 <option value="2-">MS2 and on (2-)</option>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	252 <option value="1-" selected="true">All Levels (1-)</option>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	253 </param>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	254 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	255 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	256 <option value="cwt">CantWaiT - continuous wavelet transform</option>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	257 </param>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	258 </when>
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	259 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	260
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	261 <conditional name="precursor_refinement">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	262 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	263 <when value="false"></when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	264 <when value="true">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	265 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	266 <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+">
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	267 <sanitizer>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	268 <valid initial="string.letters" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	269 </sanitizer>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	270 </param>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	271 <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10.">
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	272 <sanitizer>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	273 <valid initial="string.letters,string.digits">
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	274 <add value="-" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	275 </valid>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	276 </sanitizer>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	277 </param>
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	278 <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	279 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	280 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	281 <option value="1">MS1 Only (1)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	282 <option value="2">MS2 Only (2)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	283 <option value="2-">MS2 and on (2-)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	284 <option value="1-" selected="true">All Levels (1-)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	285 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	286 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	287 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	288
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	289 <conditional name="charge_state_calculation">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	290 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	291 <option value="false">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	292 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	293 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	294 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	295 <when value="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	296 <when value="predictor">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	297 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	298 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	299 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	300 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	301 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for "known" charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	302 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	303 <when value="turbocharger">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	304 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	305 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	306 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	307 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	308 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	309 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	310 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	311 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	312 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	313
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	314 <repeat name="thresholds" title="Filter by Threshold">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	315 <param type="select" label="Specify threshold on" name="threshold_type" help="">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	316 <option value="count">Peak count</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	317 <option value="count-after-ties">Peak count (after ties)</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	318 <option value="absolute">Peak absolute intensity</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	319 <option value="bpi-relative">Fraction of base peak intensity</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	320 <option value="tic-relative">Fraction of total ion current</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	321 <option value="tic-fraction">Aggregate fraction of total ion current</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	322 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	323 <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the "Aggregated fraction" method, peaks are accepted until this fraction of the TIC is accounted for." />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	324 <param type="select" label="Keep" name="orientation">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	325 <option value="most-intense">Most intense peaks</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	326 <option value="least-intense">Least intense peaks</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	327 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	328 </repeat>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	329
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	330 <conditional name="filter_mz_windows">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	331 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	332 <when value="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	333 <when value="true">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	334 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	335 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	336 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	337 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	338
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	339 <conditional name="etd_filtering">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	340 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	341 <when value="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	342 <when value="true">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	343 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	344 <option value="true" selected="true">yes</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	345 <option value="false">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	346 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	347 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	348 <option value="true" selected="true">yes</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	349 <option value="false">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	350 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	351 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	352 <option value="true" selected="true">yes</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	353 <option value="false">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	354 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	355 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	356 <option value="true" selected="true">yes</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	357 <option value="false">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	358 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	359 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	360 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	361 <option value="MZ" selected="true">mz</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	362 <option value="PPM">ppm</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	363 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	364 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	365 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	366
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	367 <conditional name="ms2denoise">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	368 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	369 <when value="true">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	370 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	371 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	372 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	373 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	374 <when value="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	375 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	376
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	377 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	378
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	379 </section>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	380
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	381
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	382 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	383
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	384 <param name="activation" type="select" label="Filter by Activation">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	385 <option value="false" selected="true">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	386 <option value="ETD">ETD</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	387 <option value="CID">CID</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	388 <option value="SA">SA</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	389 <option value="HCD">HCD</option>
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	390 <option value="BIRD">BIRD</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	391 <option value="ECD">ECD</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	392 <option value="IRMPD">IRMPD</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	393 <option value="PD">PD</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	394 <option value="PSD">PSD</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	395 <option value="PQD">PQD</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	396 <option value="SID">SID</option>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	397 <option value="SORI">SORI</option>
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	398 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	399
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	400 <repeat name="indices" title="Filter Scan Indices">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	401 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	402 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	403 </repeat>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	404
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	405 <repeat name="scan_numbers" title="Filter Scan Numbers">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	406 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	407 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	408 </repeat>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	409
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	410 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	411
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	412 <conditional name="filter_ms_levels">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	413 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	414 <when value="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	415 <when value="true">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	416 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	417 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	418 </when>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	419 </conditional>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	420
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	421 <param name="polarity" type="select" label="Filter by Polarity">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	422 <option value="false" selected="true">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	423 <option value="positive">positive</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	424 <option value="negative">negative</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	425 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	426
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	427 <param name="analyzer" type="select" label="Filter by Analyzer">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	428 <option value="false" selected="true">no</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	429 <option value="quad">Quadrupole</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	430 <option value="orbi">Orbitrap</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	431 <option value="FT">Fourier-transform</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	432 <option value="IT">Ion trap</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	433 <option value="TOF">Time of flight</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	434 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	435 </section>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	436
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	437 <section name="general_options" title="General Options">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	438 <param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	439
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	440 <conditional name="scan_summing">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	441 <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	442 <when value="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	443 <when value="true">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	444 <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	445 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	446 <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	447 </when>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	448 </conditional>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	449
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	450 <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	451 <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	452 <param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	453 <param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	454
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	455 <conditional name="multi_run_output">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	456 <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	457 <when value="false">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	458 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	459 </when>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	460 <when value="true">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	461 <repeat name="run_index_set" title="Select runs for multi-run sources" help="For multi-run sources (e.g. WIFF), select only the specified run indices">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	462 <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	463 <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	464 </repeat>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	465 </when>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	466 </conditional>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	467 </section>
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	468
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	469 <section name="settings" title="Output Encoding Settings">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	470 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	471 <option value="64" selected="true">64</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	472 <option value="32">32</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	473 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	474 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	475 <option value="64">64</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	476 <option value="32" selected="true">32</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	477 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	478 <param type="select" name="binary_compression" label="Binary data compression">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	479 <option value="false">None</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	480 <option value="zlib" selected="true">zlib</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	481 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	482 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	483 <option value="numpressLinear">numpressLinear only</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	484 <option value="numpressPic">numpressPic only</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	485 <option value="numpressSlof">numpressSlof only</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	486 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	487 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	488 </section>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	489 </xml>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	490
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	491 <xml name="msconvertOutput">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	492 <outputs>
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	493 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	494 <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter>
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	495 <change_format>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	496 <when input="output_type" value="mz5" format="mz5" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	497 <when input="output_type" value="mzXML" format="mzxml" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	498 <when input="output_type" value="ms2" format="ms2" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	499 <when input="output_type" value="mgf" format="mgf" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	500 </change_format>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	501 </data>
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	502 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	503 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	504 </data>
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	505 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	506 <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	507 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	508 </collection>
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	509 </outputs>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	510 </xml>
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	511
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	512
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	513 <xml name="msconvert_tests">
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	514 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	515 <param name="input" value="small.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	516 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	517 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	518 <param name="pick_peaks" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	519 <param name="pick_peaks_algorithm" value="cwt" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	520 <param name="pick_peaks_ms_levels" value="1-" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	521 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	522 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	523 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	524 <param name="input" value="small.RAW" ftype="thermo.raw" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	525 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	526 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	527 <param name="pick_peaks" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	528 <param name="pick_peaks_algorithm" value="vendor" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	529 <param name="pick_peaks_ms_levels" value="1-" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	530 <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	531 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	532 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	533 <param name="input" value="ThyroglobMRM000003.d.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	534 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	535 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	536 <param name="combineIonMobilitySpectra" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	537 <param name="do_scan_summing" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	538 <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	539 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	540 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	541 <param name="input" value="MassLynxTest.raw.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	542 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	543 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	544 <output name="output" file="MassLynxTest.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	545 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	546 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	547 <param name="input" value="AgilentMassHunterTest.d.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	548 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	549 <param name="output_type" value="mzXML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	550 <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	551 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	552 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	553 <param name="input" value="BrukerBafTest.d.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	554 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	555 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	556 <param name="pick_peaks" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	557 <param name="pick_peaks_algorithm" value="vendor" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	558 <param name="pick_peaks_ms_levels" value="1-" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	559 <output name="output" file="BrukerBafTest.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	560 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	561 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	562 <param name="input" value="SciexTest.wiff.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	563 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	564 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	565 <param name="do_multi_run_output" value="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	566 <param name="runIndexSet" value="0" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	567 <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	568 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	569 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	570 <param name="input" value="SciexTest.wiff.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	571 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	572 <param name="output_type" value="mzXML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	573 <param name="do_multi_run_output" value="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	574 <param name="runIndexSet" value="0" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	575 <param name="indices_0\|from" value="0" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	576 <param name="indices_0\|to" value="499" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	577 <param name="srmAsSpectra" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	578 <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	579 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	580 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	581 <param name="input" value="SciexTest.wiff.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	582 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	583 <param name="output_type" value="mzXML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	584 <param name="do_multi_run_output" value="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	585 <param name="runIndexSet" value="1" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	586 <param name="indices_0\|from" value="0" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	587 <param name="indices_0\|to" value="499" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	588 <param name="srmAsSpectra" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	589 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	590 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	591 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	592 <param name="input" value="SciexTest.wiff.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	593 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	594 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	595 <param name="do_multi_run_output" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	596 <param name="run_index_set_0\|from" value="0" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	597 <param name="run_index_set_0\|to" value="1" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	598 <output_collection name="multi_run_output_list" type="list">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	599 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	600 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	601 </output_collection>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	602 </test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	603 <test>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	604 <param name="input" value="SciexTest.wiff.tar" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	605 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	606 <param name="output_type" value="mzML" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	607 <param name="do_multi_run_output" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	608 <output_collection name="multi_run_output_list" type="list">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	609 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	610 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	611 </output_collection>
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	612 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	613
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	614 <!-- this data file only has profile MS1, so the result is the same -->
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	615 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	616 <param name="input" value="small.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	617 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	618 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	619 <param name="pick_peaks" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	620 <param name="pick_peaks_algorithm" value="cwt" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	621 <param name="pick_peaks_ms_levels" value="1" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	622 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	623 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	624 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	625 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	626 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	627 <param name="output_type" value="mz5" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	628 <param name="mz_encoding" value="64" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	629 <param name="intensity_encoding" value="64" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	630 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	631 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	632 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	633 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	634 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	635 <param name="output_type" value="mzXML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	636 <param name="mz_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	637 <param name="intensity_encoding" value="32" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	638 <output name="output" file="small-zlib-32.mzXML" lines_diff="6" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	639 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	640 <!-- TODO: how to test gzipped output?
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	641 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	642 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	643 <param name="output_type" value="mzXML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	644 <param name="mz_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	645 <param name="intensity_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	646 <param name="binary_compression" value="false" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	647 <param name="gzip_compression" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	648 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	649 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	650 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	651 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	652 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	653 <param name="mz_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	654 <param name="intensity_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	655 <param name="binary_compression" value="false" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	656 <param name="gzip_compression" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	657 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	658 </test>-->
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	659
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	660 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	661 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	662 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	663 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	664 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	665 <output name="output" file="small-numpressLP.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	666 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	667
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	668 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	669 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	670 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	671 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	672 <param name="binary_compression" value="numpressLinearSlof" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	673 <output name="output" file="small-numpressLS.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	674 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	675
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	676 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	677 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	678 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	679 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	680 <param name="binary_compression" value="numpressLinear" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	681 <output name="output" file="small-numpressL.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	682 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	683
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	684 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	685 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	686 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	687 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	688 <param name="binary_compression" value="numpressPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	689 <output name="output" file="small-numpressP.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	690 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	691
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	692 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	693 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	694 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	695 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	696 <param name="binary_compression" value="numpressSlof" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	697 <output name="output" file="small-numpressS.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	698 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	699
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	700 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	701 <param name="input" value="Rpal_01.mz5" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	702 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	703 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	704 <param name="binary_compression" value="numpressLinearPic" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	705 <param name="use_mzrefinement" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	706 <param name="input_ident" value="Rpal_01.pepXML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	707 <param name="thresholdScore" value="mvh" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	708 <param name="thresholdValue" value="40-" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	709 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	710 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	711 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	712
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	713 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	714 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	715 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	716 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	717 <param name="binary_compression" value="numpressLinearPic" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	718 <param name="charge_state_calculation_method" value="predictor" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	719 <param name="predictor_overrideExistingCharge" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	720 <param name="minMultipleCharge" value="2" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	721 <param name="maxMultipleCharge" value="5" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	722 <param name="singleChargeFractionTIC" value="0.95" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	723 <param name="maxKnownCharge" value="8" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	724 <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	725 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	726 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	727 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	728 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	729 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	730 <param name="binary_compression" value="numpressLinearPic" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	731 <param name="charge_state_calculation_method" value="turbocharger" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	732 <param name="minCharge" value="1" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	733 <param name="maxCharge" value="5" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	734 <param name="precursorsBefore" value="1" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	735 <param name="precursorsAfter" value="1" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	736 <param name="halfIsoWidth" value="1.5" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	737 <param name="defaultMinCharge" value="1" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	738 <param name="defaultMaxCharge" value="5" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	739 <output name="output" file="small-turbocharger.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	740 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	741 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	742 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	743 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	744 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	745 <param name="do_etd_filtering" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	746 <param name="remove_precursor" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	747 <param name="remove_charge_reduced" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	748 <param name="remove_neutral_loss" value="false" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	749 <param name="blanket_removal" value="false" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	750 <param name="matching_tolerance" value="50" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	751 <param name="matching_tolerance_units" value="ppm" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	752 <param name="binary_compression" value="numpressLinearPic" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	753 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	754 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	755 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	756 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	757 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	758 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	759 <param name="thresholds_0\|threshold_type" value="count" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	760 <param name="thresholds_0\|value" value="100" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	761 <param name="thresholds_0\|orientation" value="most-intense" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	762 <param name="thresholds_1\|threshold_type" value="absolute" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	763 <param name="thresholds_1\|value" value="1" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	764 <param name="thresholds_1\|orientation" value="most-intense" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	765 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	766 <output name="output" file="small-threshold.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	767 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	768 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	769 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	770 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	771 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	772 <param name="do_mzwindow_filter" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	773 <param name="mz_window_from" value="420" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	774 <param name="mz_window_to" value="840" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	775 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	776 <output name="output" file="small-mzWindow.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	777 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	778 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	779 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	780 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	781 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	782 <param name="denoise" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	783 <param name="num_peaks" value="10" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	784 <param name="window_width" value="40" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	785 <param name="relax" value="false" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	786 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	787 <output name="output" file="small-denoise.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	788 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	789 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	790 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	791 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	792 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	793 <param name="ms2deisotope" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	794 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	795 <output name="output" file="small-deisotope.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	796 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	797 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	798 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	799 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	800 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	801 <param name="activation" value="CID" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	802 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	803 <output name="output" file="small-activation.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	804 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	805 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	806 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	807 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	808 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	809 <param name="indices_0\|from" value="2" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	810 <param name="indices_0\|to" value="4" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	811 <param name="indices_1\|from" value="10" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	812 <param name="indices_1\|to" value="10" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	813 <param name="indices_2\|from" value="13" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	814 <param name="indices_2\|to" value="15" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	815 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	816 <output name="output" file="small-index-filter.mzML" lines_diff="32" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	817 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	818 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	819 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	820 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	821 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	822 <param name="strip_it" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	823 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	824 <output name="output" file="small-strip-it.mzML" lines_diff="100" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	825 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	826 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	827 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	828 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	829 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	830 <param name="do_ms_level_filter" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	831 <param name="ms_level_from" value="2" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	832 <param name="ms_level_to" value="2" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	833 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	834 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	835 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	836 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	837 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	838 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	839 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	840 <param name="polarity" value="positive" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	841 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	842 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	843 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	844 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	845 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	846 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	847 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	848 <param name="analyzer" value="IT" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	849 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	850 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	851 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	852 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	853 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	854 <param name="license_agreement" value="true" />
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	855 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	856 <param name="scan_numbers_0\|from" value="3" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	857 <param name="scan_numbers_0\|to" value="5" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	858 <param name="scan_numbers_1\|from" value="11" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	859 <param name="scan_numbers_1\|to" value="11" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	860 <param name="scan_numbers_2\|from" value="14" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	861 <param name="scan_numbers_2\|to" value="16" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	862 <param name="binary_compression" value="numpressLinearPic" />
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	863 <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	864 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	865 <!--<test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	866 <param name="input" value="small.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	867 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	868 <param name="binary_compression" value="numpressLinearPic" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	869 <output name="output" file="small-deisotope-poisson.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	870 </test>-->
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	871 </xml>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	872 <xml name="msconvert_help">
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	873 What it does
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	874
7 e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 galaxyp parents: 6 diff changeset	875 Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.
6 6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	876
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	877 You can view the original documentation here_.
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	878
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	879 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	880 </xml>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	881
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	882 <xml name="citations">
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	883 <citations>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	884 <citation type="doi">10.1093/bioinformatics/btn323</citation>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	885 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	886 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	887 </citations>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	888 </xml>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 5 diff changeset	889
4 158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 galaxyp parents: 3 diff changeset	890 </macros>

Mercurial > repos > galaxyp > msconvert

annotate msconvert_macros.xml @ 9:a13a1ee66232 draft