msconvert: msconvert_macros.xml annotate

annotate msconvert_macros.xml @ 0:ab59b1826345 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty

author	galaxyp
date	Thu, 22 Oct 2015 14:00:58 -0400
parents
children	987d73278bf9

rev	line source
0 ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	1 <macros>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	2 <xml name="msconvertCommand">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	3 <command>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	4 <![CDATA[
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	5 #import re
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	6 #set $output_type_str = str($output_type)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	7 #set $input_name = $input.display_name
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	8 #set $output_name = $input_name.split(".")[0] + "." + $output_type_str
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	9 ln -s '$input' '${input_name}' &&
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	10
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	11 #if $data_processing.precursor_refinement.use_mzrefinement
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	12 #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	13 ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_name}' &&
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	14 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	15
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	16 mkdir outdir &&
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	17 msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name'
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	18
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	19 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	20 #if $data_processing.peak_picking.pick_peaks
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	21 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	22 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	23
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	24 #if $data_processing.precursor_refinement.use_mzrefinement
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	25 --filter "mzRefiner $input_ident_name
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	26 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	27 thresholdScore=$data_processing.precursor_refinement.thresholdScore
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	28 thresholdValue=$data_processing.precursor_refinement.thresholdValue
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	29 thresholdStep=$data_processing.precursor_refinement.thresholdStep
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	30 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	31 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	32
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	33 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	34 --filter "chargeStatePredictor
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	35 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	36 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	37 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	38 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	39 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	40 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	41 --filter "turbocharger
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	42 minCharge=$data_processing.charge_state_calculation.minCharge
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	43 maxCharge=$data_processing.charge_state_calculation.maxCharge
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	44 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	45 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	46 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	47 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	48 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	49 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	50
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	51 #for threshold_entry in $data_processing.thresholds
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	52 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	53 #end for
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	54
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	55 #if $data_processing.filter_mz_windows.do_mzwindow_filter
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	56 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	57 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	58
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	59 #if $data_processing.etd_filtering.do_etd_filtering
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	60 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	61 $data_processing.etd_filtering.remove_charge_reduced
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	62 $data_processing.etd_filtering.remove_neutral_loss
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	63 $data_processing.etd_filtering.blanket_removal
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	64 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	65 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	66
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	67 #if $data_processing.ms2denoise.denoise
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	68 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	69 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	70
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	71 #if str($data_processing.ms2deisotope) == "true"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	72 --filter "MS2Deisotope"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	73 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	74
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	75
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	76 ## SCAN INCLUSION/EXCLUSION FILTERS
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	77 #if str($filtering.activation) != "false"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	78 --filter "activation $filtering.activation"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	79 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	80
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	81 #if len($filtering.indices) > 0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	82 --filter "index
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	83 #for $index in $filtering.indices
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	84 [${index.from},${index.to}]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	85 #end for
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	86 "
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	87 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	88
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	89 #if len($filtering.scan_numbers) > 0
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	90 --filter "scanNumber
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	91 #for $scan_number in $filtering.scan_numbers
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	92 [${scan_number.from},${scan_number.to}]
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	93 #end for
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	94 "
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	95 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	96
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	97 #if $filtering.strip_it.value
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	98 --filter "stripIT"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	99 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	100
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	101 #if $filtering.filter_ms_levels.do_ms_level_filter
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	102 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	103 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	104
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	105 #if str($filtering.polarity) != "false"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	106 --filter "polarity $filtering.polarity"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	107 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	108
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	109 #if str($filtering.analyzer) != "false"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	110 --filter "analyzer $filtering.analyzer"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	111 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	112
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	113 ## OUTPUT ENCODING
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	114 #set $mz_encoding = str($settings.mz_encoding)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	115 #set $intensity_encoding = str($settings.intensity_encoding)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	116 #if $mz_encoding == $intensity_encoding
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	117 #if $mz_encoding == "64"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	118 --64
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	119 #else
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	120 --32
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	121 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	122 #else
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	123 --mz${mz_encoding}
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	124 --inten${intensity_encoding}
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	125 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	126
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	127 #set binary_compression = str($settings.binary_compression)
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	128 #if $binary_compression == "zlib"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	129 --zlib
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	130 #else if $binary_compression == "numpressLinearPic"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	131 --numpressLinear --numpressPic
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	132 #else if $binary_compression == "numpressLinearSlof"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	133 --numpressLinear --numpressSlof
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	134 #else if $binary_compression == "numpressLinear"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	135 --numpressLinear
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	136 #else if $binary_compression == "numpressPic"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	137 --numpressPic
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	138 #else if $binary_compression == "numpressSlof"
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	139 --numpressSlof
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	140 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	141
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	142 #if $settings.gzip_compression
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	143 --gzip
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	144 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	145
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	146 &&
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	147
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	148 #if $data_processing.precursor_refinement.use_mzrefinement
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	149 mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	150 #end if
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	151
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	152 mv 'outdir/$output_name' output &&
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	153 rmdir outdir
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	154 ]]>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	155 </command>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	156 </xml>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	157
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	158 <xml name="msconvertInputParameters">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	159 <param name="output_type" type="select" label="Output Type">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	160 <option value="mz5" selected="true">mz5</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	161 <option value="mzML">mzML</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	162 <option value="mzXML">mzXML</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	163 <option value="mgf">mgf</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	164 <option value="ms2">ms2</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	165 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	166
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	167 <section name="data_processing" title="Data Processing Filters">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	168
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	169 <conditional name="peak_picking">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	170 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	171 <when value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	172 <when value="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	173 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	174 <option value="1">MS1 Only (1)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	175 <option value="2">MS2 Only (2)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	176 <option value="2-">MS2 and on (2-)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	177 <option value="1-" selected="true">All Levels (1-)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	178 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	179 <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)">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	180 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	181 <option value="cwt">CantWaiT - continuous wavelet transform</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	182 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	183 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	184 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	185
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	186 <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	187 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	188 <when value="false"></when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	189 <when value="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	190 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	191 <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+" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	192 <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." />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	193 <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)." />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	194 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	195 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	196 <option value="1">MS1 Only (1)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	197 <option value="2">MS2 Only (2)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	198 <option value="2-">MS2 and on (2-)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	199 <option value="1-" selected="true">All Levels (1-)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	200 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	201 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	202 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	203
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	204 <conditional name="charge_state_calculation">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	205 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	206 <option value="false">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	207 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	208 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	209 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	210 <when value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	211 <when value="predictor">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	212 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	213 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	214 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	215 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	216 <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" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	217 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	218 <when value="turbocharger">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	219 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	220 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	221 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	222 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	223 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	224 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	225 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	226 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	227 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	228
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	229 <repeat name="thresholds" title="Filter by Threshold">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	230 <param type="select" label="Specify threshold on" name="threshold_type" help="">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	231 <option value="count">Peak count</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	232 <option value="count-after-ties">Peak count (after ties)</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	233 <option value="absolute">Peak absolute intensity</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	234 <option value="bpi-relative">Fraction of base peak intensity</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	235 <option value="tic-relative">Fraction of total ion current</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	236 <option value="tic-fraction">Aggregate fraction of total ion current</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	237 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	238 <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." />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	239 <param type="select" label="Keep" name="orientation">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	240 <option value="most-intense">Most intense peaks</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	241 <option value="least-intense">Least intense peaks</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	242 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	243 </repeat>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	244
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	245 <conditional name="filter_mz_windows">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	246 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	247 <when value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	248 <when value="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	249 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	250 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	251 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	252 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	253
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	254 <conditional name="etd_filtering">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	255 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	256 <when value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	257 <when value="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	258 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	259 <option value="true" selected="true">yes</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	260 <option value="false">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	261 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	262 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	263 <option value="true" selected="true">yes</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	264 <option value="false">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	265 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	266 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	267 <option value="true" selected="true">yes</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	268 <option value="false">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	269 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	270 <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)">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	271 <option value="true" selected="true">yes</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	272 <option value="false">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	273 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	274 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	275 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	276 <option value="MZ" selected="true">mz</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	277 <option value="PPM">ppm</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	278 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	279 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	280 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	281
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	282 <conditional name="ms2denoise">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	283 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	284 <when value="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	285 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	286 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	287 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	288 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	289 <when value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	290 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	291
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	292 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	293
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	294 </section>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	295
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	296
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	297 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	298
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	299 <param name="activation" type="select" label="Filter by Activation">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	300 <option value="false" selected="true">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	301 <option value="ETD">ETD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	302 <option value="CID">CID</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	303 <option value="SA">SA</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	304 <option value="HCD">HCD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	305 <option>BIRD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	306 <option>ECD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	307 <option>IRMPD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	308 <option>PD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	309 <option>PSD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	310 <option>PQD</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	311 <option>SID</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	312 <option>SORI</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	313 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	314
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	315 <repeat name="indices" title="Filter Scan Indices">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	316 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	317 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	318 </repeat>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	319
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	320 <repeat name="scan_numbers" title="Filter Scan Numbers">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	321 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	322 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	323 </repeat>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	324
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	325 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	326
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	327 <conditional name="filter_ms_levels">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	328 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	329 <when value="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	330 <when value="true">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	331 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	332 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	333 </when>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	334 </conditional>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	335
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	336 <param name="polarity" type="select" label="Filter by Polarity">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	337 <option value="false" selected="true">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	338 <option value="positive">positive</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	339 <option value="negative">negative</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	340 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	341
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	342 <param name="analyzer" type="select" label="Filter by Analyzer">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	343 <option value="false" selected="true">no</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	344 <option value="quad">Quadrupole</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	345 <option value="orbi">Orbitrap</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	346 <option value="FT">Fourier-transform</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	347 <option value="IT">Ion trap</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	348 <option value="TOF">Time of flight</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	349 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	350 </section>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	351
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	352
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	353 <section name="settings" title="Output Encoding Settings">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	354 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	355 <option value="64" selected="true">64</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	356 <option value="32">32</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	357 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	358 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	359 <option value="64">64</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	360 <option value="32" selected="true">32</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	361 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	362 <param type="select" name="binary_compression" label="Binary data compression">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	363 <option value="false">None</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	364 <option value="zlib" selected="true">zlib</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	365 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	366 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	367 <option value="numpressLinear">numpressLinear only</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	368 <option value="numpressPic">numpressPic only</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	369 <option value="numpressSlof">numpressSlof only</option>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	370 </param>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	371 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	372 </section>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	373 </xml>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	374
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	375 <xml name="msconvertOutput">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	376 <outputs>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	377 <data format="mzml" name="output" from_work_dir="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	378 <change_format>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	379 <when input="output_type" value="mz5" format="mz5" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	380 <when input="output_type" value="mzXML" format="mzxml" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	381 <when input="output_type" value="ms2" format="ms2" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	382 <when input="output_type" value="mgf" format="mgf" />
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	383 </change_format>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	384 </data>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	385 <data format="csv" name="output.refinement" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	386
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	387 </data>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	388 </outputs>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	389 </xml>
ab59b1826345 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty galaxyp parents: diff changeset	390 </macros>

Mercurial > repos > galaxyp > msconvert

annotate msconvert_macros.xml @ 0:ab59b1826345 draft