msconvert_nix: msconvert_macros.xml annotate

annotate msconvert_macros.xml @ 1:7016f1f10f42 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848

author	galaxyp
date	Tue, 14 Mar 2017 16:45:30 -0400
parents	baa6c072fccc
children

rev	line source
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	1 <macros>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	2 <xml name="generic_requirements">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	3 <requirements>
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	5 </requirements>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	6 </xml>
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	7 <token name="@VERSION@">3.0.9992</token>
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	8
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	9 <xml name="msconvertCommand">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	10 <command interpreter="python">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	11 <![CDATA[
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	12 #import re
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	13 #set $ext = $input.ext
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	14
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	15 ## sanitize display name for use as temp filename
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	16 #set basename = 'pwiz_in'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	17
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	18 #if hasattr($input, 'display_name')
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	19 ## explicit inclusion or exclusion ??
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	20 #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name)
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	21 ##set basename = $re.sub(r'[\/\\\;\\|\&\>\<]','_',$input.display_name)
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	22 #end if
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	23
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	24 msconvert_wrapper.py
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	25
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	26 #if $ext == 'wiff':
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	27 --input='${input.extra_files_path}/wiff'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	28 --input_name='${basename}.wiff'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	29 --implicit='${input.extra_files_path}/wiff_scan'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	30 --input='${input.extra_files_path}/wiff_scan'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	31 --input_name='${basename}.wiff.scan'
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	32 #else
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	33 --input='${input}'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	34 --input_name='$basename'
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	35 #end if
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	36 --output='${output}'
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	37 ## BEGIN_VERSION_DEFAULT
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	38 --fromextension=$ext
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	39 ## END_VERSION_DEFAULT
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	40 --toextension=${output_type}
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	41
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	42 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	43 #if $data_processing.precursor_refinement.use_mzrefinement
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	44 #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	45 --ident='$data_processing.precursor_refinement.input_ident'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	46 --ident_name='$input_ident_name'
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	47 --refinement='$output_refinement'
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	48 --filter "mzRefiner $input_ident_name
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	54 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	55
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	56 #if $data_processing.peak_picking.pick_peaks
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	58 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	59
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	61 --filter "chargeStatePredictor
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	63 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	64 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	65 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	66 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	67 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	68 --filter "turbocharger
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	69 minCharge=$data_processing.charge_state_calculation.minCharge
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	70 maxCharge=$data_processing.charge_state_calculation.maxCharge
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	71 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	72 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	73 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	76 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	77
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	78 #for threshold_entry in $data_processing.thresholds
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	80 #end for
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	81
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	84 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	85
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	86 #if $data_processing.etd_filtering.do_etd_filtering
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	88 $data_processing.etd_filtering.remove_charge_reduced
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	89 $data_processing.etd_filtering.remove_neutral_loss
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	90 $data_processing.etd_filtering.blanket_removal
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	92 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	93
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	94 #if $data_processing.ms2denoise.denoise
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	96 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	97
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	98 #if str($data_processing.ms2deisotope) == "true"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	99 --filter "MS2Deisotope"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	100 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	101
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	102
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	103 ## SCAN INCLUSION/EXCLUSION FILTERS
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	104 #if str($filtering.activation) != "false"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	105 --filter "activation $filtering.activation"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	106 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	107
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	108 #if len($filtering.indices) > 0
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	109 --filter "index
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	110 #for $index in $filtering.indices
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	111 [${index.from},${index.to}]
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	112 #end for
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	113 "
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	114 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	115
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	116 #if len($filtering.scan_numbers) > 0
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	117 --filter "scanNumber
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	118 #for $scan_number in $filtering.scan_numbers
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	119 [${scan_number.from},${scan_number.to}]
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	120 #end for
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	121 "
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	122 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	123
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	124 #if $filtering.strip_it.value
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	125 --filter "stripIT"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	126 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	127
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	128 #if $filtering.filter_ms_levels.do_ms_level_filter
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	130 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	131
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	132 #if str($filtering.polarity) != "false"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	133 --filter "polarity $filtering.polarity"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	134 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	135
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	136 #if str($filtering.analyzer) != "false"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	137 --filter "analyzer $filtering.analyzer"
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	138 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	139
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	140 ## OUTPUT ENCODING
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	141 --
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	142 #set $mz_encoding = str($settings.mz_encoding)
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	143 #set $intensity_encoding = str($settings.intensity_encoding)
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	144 #if $mz_encoding == $intensity_encoding
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	145 #if $mz_encoding == "64"
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	146 --64
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	147 #else
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	148 --32
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	149 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	150 #else
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	151 --mz${mz_encoding}
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	152 --inten${intensity_encoding}
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	153 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	154
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	155 #set binary_compression = str($settings.binary_compression)
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	156 #if $binary_compression == "zlib"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	157 --zlib
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	158 #else if $binary_compression == "numpressLinearPic"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	159 --numpressLinear --numpressPic
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	160 #else if $binary_compression == "numpressLinearSlof"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	161 --numpressLinear --numpressSlof
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	162 #else if $binary_compression == "numpressLinear"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	163 --numpressLinear
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	164 #else if $binary_compression == "numpressPic"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	165 --numpressPic
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	166 #else if $binary_compression == "numpressSlof"
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	167 --numpressSlof
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	168 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	169
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	170 #if $settings.gzip_compression
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	171 --gzip
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	172 #end if
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	173
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	174 ]]>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	175 </command>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	176 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	177
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	178 <xml name="msconvertInputParameters">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	179 <param name="output_type" type="select" label="Output Type">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	180 <option value="mz5" selected="true">mz5</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	181 <option value="mzML">mzML</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	182 <option value="mzXML">mzXML</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	183 <option value="mgf">mgf</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	184 <option value="ms2">ms2</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	185 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	186
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	187 <section name="data_processing" title="Data Processing Filters">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	188
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	189 <conditional name="peak_picking">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	190 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	191 <when value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	192 <when value="true">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	193 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	194 <option value="1">MS1 Only (1)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	195 <option value="2">MS2 Only (2)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	196 <option value="2-">MS2 and on (2-)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	197 <option value="1-" selected="true">All Levels (1-)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	198 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	199 <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)">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	200 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	201 <option value="cwt">CantWaiT - continuous wavelet transform</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	202 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	203 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	204 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	205
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	206 <conditional name="precursor_refinement">
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	208 <when value="false"></when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	209 <when value="true">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	211 <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+">
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	212 <sanitizer>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	213 <valid initial="string.letters" />
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	214 </sanitizer>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	215 </param>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	216 <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.">
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	217 <sanitizer>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	218 <valid initial="string.letters,string.digits">
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	219 <add value="-" />
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	220 </valid>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	221 </sanitizer>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	222 </param>
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	223 <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)." />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	224 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	225 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	226 <option value="1">MS1 Only (1)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	227 <option value="2">MS2 Only (2)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	228 <option value="2-">MS2 and on (2-)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	229 <option value="1-" selected="true">All Levels (1-)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	230 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	231 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	232 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	233
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	234 <conditional name="charge_state_calculation">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	235 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	236 <option value="false">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	237 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	238 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	239 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	240 <when value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	241 <when value="predictor">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	242 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	243 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	244 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	245 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	246 <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" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	247 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	248 <when value="turbocharger">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	249 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	250 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	251 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	252 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	253 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	254 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	255 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	256 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	257 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	258
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	259 <repeat name="thresholds" title="Filter by Threshold">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	260 <param type="select" label="Specify threshold on" name="threshold_type" help="">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	261 <option value="count">Peak count</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	262 <option value="count-after-ties">Peak count (after ties)</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	263 <option value="absolute">Peak absolute intensity</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	264 <option value="bpi-relative">Fraction of base peak intensity</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	265 <option value="tic-relative">Fraction of total ion current</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	266 <option value="tic-fraction">Aggregate fraction of total ion current</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	267 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	268 <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." />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	269 <param type="select" label="Keep" name="orientation">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	270 <option value="most-intense">Most intense peaks</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	271 <option value="least-intense">Least intense peaks</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	272 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	273 </repeat>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	274
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	275 <conditional name="filter_mz_windows">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	276 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	277 <when value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	278 <when value="true">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	279 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	280 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	281 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	282 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	283
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	284 <conditional name="etd_filtering">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	285 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	286 <when value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	287 <when value="true">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	288 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	289 <option value="true" selected="true">yes</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	290 <option value="false">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	291 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	292 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	293 <option value="true" selected="true">yes</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	294 <option value="false">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	295 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	296 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	297 <option value="true" selected="true">yes</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	298 <option value="false">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	299 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	300 <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)">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	301 <option value="true" selected="true">yes</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	302 <option value="false">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	303 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	304 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	305 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	306 <option value="MZ" selected="true">mz</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	307 <option value="PPM">ppm</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	308 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	309 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	310 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	311
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	312 <conditional name="ms2denoise">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	313 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	314 <when value="true">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	315 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	316 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	317 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	318 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	319 <when value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	320 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	321
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	322 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	323
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	324 </section>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	325
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	326
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	327 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	328
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	329 <param name="activation" type="select" label="Filter by Activation">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	330 <option value="false" selected="true">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	331 <option value="ETD">ETD</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	332 <option value="CID">CID</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	333 <option value="SA">SA</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	334 <option value="HCD">HCD</option>
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	335 <option value="BIRD">BIRD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	336 <option value="ECD">ECD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	337 <option value="IRMPD">IRMPD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	338 <option value="PD">PD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	339 <option value="PSD">PSD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	340 <option value="PQD">PQD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	341 <option value="SID">SID</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	342 <option value="SORI">SORI</option>
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	343 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	344
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	345 <repeat name="indices" title="Filter Scan Indices">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	346 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	347 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	348 </repeat>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	349
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	350 <repeat name="scan_numbers" title="Filter Scan Numbers">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	351 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	352 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	353 </repeat>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	354
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	355 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	356
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	357 <conditional name="filter_ms_levels">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	358 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	359 <when value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	360 <when value="true">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	361 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	362 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	363 </when>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	364 </conditional>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	365
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	366 <param name="polarity" type="select" label="Filter by Polarity">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	367 <option value="false" selected="true">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	368 <option value="positive">positive</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	369 <option value="negative">negative</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	370 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	371
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	372 <param name="analyzer" type="select" label="Filter by Analyzer">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	373 <option value="false" selected="true">no</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	374 <option value="quad">Quadrupole</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	375 <option value="orbi">Orbitrap</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	376 <option value="FT">Fourier-transform</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	377 <option value="IT">Ion trap</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	378 <option value="TOF">Time of flight</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	379 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	380 </section>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	381
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	382
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	383 <section name="settings" title="Output Encoding Settings">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	384 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	385 <option value="64" selected="true">64</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	386 <option value="32">32</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	387 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	388 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	389 <option value="64">64</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	390 <option value="32" selected="true">32</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	391 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	392 <param type="select" name="binary_compression" label="Binary data compression">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	393 <option value="false">None</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	394 <option value="zlib" selected="true">zlib</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	395 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	396 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	397 <option value="numpressLinear">numpressLinear only</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	398 <option value="numpressPic">numpressPic only</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	399 <option value="numpressSlof">numpressSlof only</option>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	400 </param>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	401 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	402 </section>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	403 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	404
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	405 <xml name="msconvertOutput">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	406 <outputs>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	407 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	408 <change_format>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	409 <when input="output_type" value="mz5" format="mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	410 <when input="output_type" value="mzXML" format="mzxml" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	411 <when input="output_type" value="ms2" format="ms2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	412 <when input="output_type" value="mgf" format="mgf" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	413 </change_format>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	414 </data>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	415 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	416 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	417 </data>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	418 </outputs>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	419 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	420
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	421
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	422 <xml name="msconvert_tests">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	423 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	424 <param name="input" value="small.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	425 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	426 <param name="pick_peaks" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	427 <param name="pick_peaks_algorithm" value="cwt" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	428 <param name="pick_peaks_ms_levels" value="1-" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	430 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	431
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	432 <!-- this data file only has profile MS1, so the result is the same -->
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	433 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	434 <param name="input" value="small.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	435 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	436 <param name="pick_peaks" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	437 <param name="pick_peaks_algorithm" value="cwt" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	438 <param name="pick_peaks_ms_levels" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	439 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	440 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	441 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	442 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	443 <param name="output_type" value="mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	444 <param name="mz_encoding" value="64" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	445 <param name="intensity_encoding" value="64" />
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	446 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	447 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	448 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	449 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	450 <param name="output_type" value="mzXML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	451 <param name="mz_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	452 <param name="intensity_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	453 <output name="output" file="small-zlib-32.mzXML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	454 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	455 <!-- TODO: how to test gzipped output?
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	456 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	457 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	458 <param name="output_type" value="mzXML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	459 <param name="mz_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	460 <param name="intensity_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	461 <param name="binary_compression" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	462 <param name="gzip_compression" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	463 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	464 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	465 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	467 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	468 <param name="mz_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	469 <param name="intensity_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	470 <param name="binary_compression" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	471 <param name="gzip_compression" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	472 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	473 </test>-->
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	474
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	475 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	476 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	477 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	478 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	479 <output name="output" file="small-numpressLP.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	480 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	481
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	482 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	483 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	484 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	485 <param name="binary_compression" value="numpressLinearSlof" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	486 <output name="output" file="small-numpressLS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	487 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	488
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	489 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	490 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	491 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	492 <param name="binary_compression" value="numpressLinear" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	493 <output name="output" file="small-numpressL.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	494 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	495
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	496 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	497 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	498 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	499 <param name="binary_compression" value="numpressPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	500 <output name="output" file="small-numpressP.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	501 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	502
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	503 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	504 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	505 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	506 <param name="binary_compression" value="numpressSlof" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	507 <output name="output" file="small-numpressS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	508 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	509
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	510 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	511 <param name="input" value="Rpal_01.mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	512 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	513 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	514 <param name="use_mzrefinement" value="true" />
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	515 <param name="input_ident" value="Rpal_01.pepXML" />
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	516 <param name="thresholdScore" value="mvh" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	517 <param name="thresholdValue" value="40-" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	518 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
1 7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 galaxyp parents: 0 diff changeset	519 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
0 baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	520 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	521
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	522 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	523 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	524 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	525 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	526 <param name="charge_state_calculation_method" value="predictor" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	527 <param name="predictor_overrideExistingCharge" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	528 <param name="minMultipleCharge" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	529 <param name="maxMultipleCharge" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	530 <param name="singleChargeFractionTIC" value="0.95" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	531 <param name="maxKnownCharge" value="8" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	532 <output name="output" file="small-chargeStatePredictor.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	533 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	534 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	535 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	536 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	537 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	538 <param name="charge_state_calculation_method" value="turbocharger" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	539 <param name="minCharge" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	540 <param name="maxCharge" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	541 <param name="precursorsBefore" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	542 <param name="precursorsAfter" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	543 <param name="halfIsoWidth" value="1.5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	544 <param name="defaultMinCharge" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	545 <param name="defaultMaxCharge" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	546 <output name="output" file="small-turbocharger.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	547 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	548 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	549 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	550 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	551 <param name="do_etd_filtering" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	552 <param name="remove_precursor" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	553 <param name="remove_charge_reduced" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	554 <param name="remove_neutral_loss" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	555 <param name="blanket_removal" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	556 <param name="matching_tolerance" value="50" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	557 <param name="matching_tolerance_units" value="ppm" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	558 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	559 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	560 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	561 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	562 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	563 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	564 <param name="thresholds_0\|threshold_type" value="count" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	565 <param name="thresholds_0\|value" value="100" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	566 <param name="thresholds_0\|orientation" value="most-intense" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	567 <param name="thresholds_1\|threshold_type" value="absolute" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	568 <param name="thresholds_1\|value" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	569 <param name="thresholds_1\|orientation" value="most-intense" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	570 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	571 <output name="output" file="small-threshold.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	572 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	573 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	574 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	575 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	576 <param name="do_mzwindow_filter" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	577 <param name="mz_window_from" value="420" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	578 <param name="mz_window_to" value="840" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	579 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	580 <output name="output" file="small-mzWindow.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	581 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	582 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	584 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	585 <param name="denoise" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	586 <param name="num_peaks" value="10" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	587 <param name="window_width" value="40" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	588 <param name="relax" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	589 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	590 <output name="output" file="small-denoise.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	591 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	592 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	593 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	594 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	595 <param name="ms2deisotope" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	596 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	597 <output name="output" file="small-deisotope.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	598 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	599 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	600 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	601 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	602 <param name="activation" value="CID" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	603 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	604 <output name="output" file="small-activation.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	605 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	606 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	607 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	608 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	609 <param name="indices_0\|from" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	610 <param name="indices_0\|to" value="4" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	611 <param name="indices_1\|from" value="10" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	612 <param name="indices_1\|to" value="10" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	613 <param name="indices_2\|from" value="13" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	614 <param name="indices_2\|to" value="15" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	615 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	616 <output name="output" file="small-index-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	617 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	618 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	619 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	620 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	621 <param name="strip_it" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	622 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	623 <output name="output" file="small-strip-it.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	624 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	625 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	626 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	627 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	628 <param name="do_ms_level_filter" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	629 <param name="ms_level_from" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	630 <param name="ms_level_to" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	631 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	632 <output name="output" file="small-ms-level-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	633 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	634 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	635 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	636 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	637 <param name="polarity" value="positive" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	638 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	639 <output name="output" file="small-polarity-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	640 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	641 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	642 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	643 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	644 <param name="analyzer" value="IT" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	645 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	646 <output name="output" file="small-analyzer-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	647 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	648 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	649 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	650 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	651 <param name="scan_numbers_0\|from" value="3" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	652 <param name="scan_numbers_0\|to" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	653 <param name="scan_numbers_1\|from" value="11" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	654 <param name="scan_numbers_1\|to" value="11" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	655 <param name="scan_numbers_2\|from" value="14" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	656 <param name="scan_numbers_2\|to" value="16" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	657 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	658 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	659 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	660 <!--<test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	661 <param name="input" value="small.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	662 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	663 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	664 <output name="output" file="small-deisotope-poisson.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	665 </test>-->
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	666 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	667 <xml name="msconvert_help">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	668 What it does
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	669
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	670 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	671
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	672 You can view the original documentation here_.
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	673
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	674 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	675 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	676
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	677 <xml name="citations">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	678 <citations>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	679 <citation type="doi">10.1093/bioinformatics/btn323</citation>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	680 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	681 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	682 </citations>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	683 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	684
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty galaxyp parents: diff changeset	685 </macros>

Mercurial > repos > galaxyp > msconvert_nix

annotate msconvert_macros.xml @ 1:7016f1f10f42 draft