dia_umpire: dia_umpire_se.xml annotate

annotate dia_umpire_se.xml @ 4:e8822850243a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f

author	galaxyp
date	Mon, 04 Mar 2019 11:49:42 -0500
parents	6caa9011f245
children

rev	line source
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	1 <tool id="dia_umpire_se" name="DIA_Umpire_SE" version="@VERSION@.0">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	2 <description>DIA signal extraction</description>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	3 <macros>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	4 <import>dia_umpire_macros.xml</import>
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	5 </macros>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	6 <expand macro="requirements" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	7 <expand macro="stdio" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	8 <command>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	9 <![CDATA[
4 e8822850243a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 3 diff changeset	10 #set $output_dir = 'gx_path'
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	11 #import re
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	12 mkdir '$output_dir'
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	13 && cat $se_config > $se_params
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	14 && echo " " >> $se_params
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	15 && echo "Thread = \$GALAXY_SLOTS" >> $se_params
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	16 #if $input_prefix and len($input_prefix.strip()) > 0:
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	17 #set $input_path = str($output_dir) + '/' + $input_prefix.__str__ + '_rep' + str($i + 1) + '.mzXML'
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	18 #else:
4 e8822850243a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 3 diff changeset	19 #set $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.element_identifier)) + '.mzXML'
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	20 #end if
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	21 && ln -s '${input}' '$input_path'
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	22 && dia_umpire_se '$input_path' '$se_params'
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	23 && cat $output_dir/*.log >> "$logfile"
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	24 #if not $mgfs_as_collection:
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	25 && cp "$output_dir/"*_Q1.mgf '$q1_mgf'
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	26 && cp "$output_dir/"*_Q2.mgf '$q2_mgf'
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	27 && cp "$output_dir/"*_Q3.mgf '$q3_mgf'
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	28 #end if
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	29 #if $ExportPrecursorPeak:
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	30 && cp "$output_dir/"*PeakCluster.csv '$PrecursorPeak'
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	31 #end if
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	32 ]]>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	33 </command>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	34 <configfiles>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	35 <configfile name="se_config"><![CDATA[#slurp
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	36 #DIA-Umpire (version @VERSION@)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	37 #Data Independent Acquisition data processing and analysis package (Signal extraction module)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	38
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	39 #import re
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	40 #if $input_prefix:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	41 #set $input_path = $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML"
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	42 #else:
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	43 #set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + ".mzXML"
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	44 #end if
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	45 # $input.name $input_path $input
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	46
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	47 #No of threads
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	48 Thread = 6
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	49
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	50 #Report peak
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	51 ExportPrecursorPeak = $ExportPrecursorPeak
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	52 ExportFragmentPeak = $ExportFragmentPeak
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	53
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	54 #Signal extraction parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	55 #if $instrument.model == 'Thermo_Orbitrap':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	56 SE.MS1PPM = #if $instrument.SE_MS1PPM then $instrument.SE_MS1PPM else 5#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	57 SE.MS2PPM = #if $instrument.SE_MS2PPM then $instrument.SE_MS2PPM else 5#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	58 SE.Resolution = #if $instrument.SE_Resolution then $instrument.SE_Resolution else 17000#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	59 SE.StartCharge = #if $instrument.SE_StartCharge then $instrument.SE_StartCharge else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	60 SE.EndCharge = #if $instrument.SE_EndCharge then $instrument.SE_EndCharge else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	61 SE.MS2StartCharge = #if $instrument.SE_MS2StartCharge then $instrument.SE_MS2StartCharge else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	62 SE.MS2EndCharge = #if $instrument.SE_MS2EndCharge then $instrument.SE_MS2EndCharge else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	63 #else if $instrument.model == 'AB_SCIEX_Triple_TOF_5600':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	64 SE.MS1PPM = #if $instrument.SE_MS1PPM then $instrument.SE_MS1PPM else 30#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	65 SE.MS2PPM = #if $instrument.SE_MS2PPM then $instrument.SE_MS2PPM else 40#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	66 SE.Resolution = #if $instrument.SE_Resolution then $instrument.SE_Resolution else 17000#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	67 SE.StartCharge = #if $instrument.SE_StartCharge then $instrument.SE_StartCharge else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	68 SE.EndCharge = #if $instrument.SE_EndCharge then $instrument.SE_EndCharge else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	69 SE.MS2StartCharge = #if $instrument.SE_MS2StartCharge then $instrument.SE_MS2StartCharge else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	70 SE.MS2EndCharge = #if $instrument.SE_MS2EndCharge then $instrument.SE_MS2EndCharge else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	71 #else:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	72 SE.MS1PPM = #if $instrument.SE_MS1PPM then $instrument.SE_MS1PPM else 30#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	73 SE.MS2PPM = #if $instrument.SE_MS2PPM then $instrument.SE_MS2PPM else 40#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	74 SE.Resolution = #if $instrument.SE_Resolution then $instrument.SE_Resolution else 17000#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	75 SE.StartCharge = #if $instrument.SE_StartCharge then $instrument.SE_StartCharge else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	76 SE.EndCharge = #if $instrument.SE_EndCharge then $instrument.SE_EndCharge else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	77 SE.MS2StartCharge = #if $instrument.SE_MS2StartCharge then $instrument.SE_MS2StartCharge else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	78 SE.MS2EndCharge = #if $instrument.SE_MS2EndCharge then $instrument.SE_MS2EndCharge else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	79 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	80
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	81 #if $frag_settings.advanced == 'yes':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	82 #Fragment grouping parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	83 RPmax = #if $frag_settings.RPmax then $frag_settings.RPmax else 25#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	84 RFmax = #if $frag_settings.RFmax then $frag_settings.RFmax else 300#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	85 CorrThreshold = #if $frag_settings.CorrThreshold then $frag_settings.CorrThreshold else 0.2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	86 DeltaApex = #if $frag_settings.DeltaApex then $frag_settings.DeltaApex else 0.6#
2 b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	87 RTOverlap = #if $frag_settings.RTOverlap then $frag_settings.RTOverlap else 0.3#
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	88 AdjustFragIntensity = #if $frag_settings.AdjustFragIntensity then $frag_settings.AdjustFragIntensity else true#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	89 BoostComplementaryIon = #if $frag_settings.BoostComplementaryIon then $frag_settings.BoostComplementaryIon else true#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	90 #else:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	91 #Fragment grouping parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	92 RPmax = 25
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	93 RFmax = 300
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	94 CorrThreshold = 0.2
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	95 DeltaApex = 0.6
2 b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	96 RTOverlap = 0.3
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	97 AdjustFragIntensity = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	98 BoostComplementaryIon = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	99 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	100
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	101 #if $se_settings.advanced == 'yes':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	102 #Signal extraction parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	103 SE.SN = #if $se_settings.SE_SN then $se_settings.SE_SN else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	104 SE.MS2SN = #if $se_settings.SE_MS2SN then $se_settings.SE_MS2SN else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	105 SE.MinMSIntensity = #if $se_settings.SE_MinMSIntensity then $se_settings.SE_MinMSIntensity else 10#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	106 SE.MinMSMSIntensity = #if $se_settings.SE_MinMSMSIntensity then $se_settings.SE_MinMSMSIntensity else 10#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	107 SE.MaxCurveRTRange = #if $se_settings.SE_MaxCurveRTRange then $se_settings.SE_MaxCurveRTRange else 1#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	108 SE.NoMissedScan = #if $se_settings.SE_NoMissedScan then $se_settings.SE_NoMissedScan else 1#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	109 SE.MinFrag = #if $se_settings.SE_MinFrag then $se_settings.SE_MinFrag else 10#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	110 SE.EstimateBG = #if $se_settings.SE_EstimateBG then $se_settings.SE_EstimateBG else true#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	111 SE.MinNoPeakCluster = #if $se_settings.SE_MinNoPeakCluster then $se_settings.SE_MinNoPeakCluster else 2#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	112 SE.MaxNoPeakCluster = #if $se_settings.SE_MaxNoPeakCluster then $se_settings.SE_MaxNoPeakCluster else 4#
2 b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	113 SE.StartRT = #if $se_settings.SE_StartRT then $se_settings.SE_MaxNoPeakCluster else 0#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	114 SE.EndRT = #if $se_settings.SE_EndRT then $se_settings.SE_EndRT else 9999#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	115 SE.MinMZ = #if $se_settings.SE_MinMZ then $se_settings.SE_MinMZ else 200#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	116 SE.MinPrecursorMass = #if $se_settings.SE_MinPrecursorMass then $se_settings.SE_MinPrecursorMass else 700#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	117 SE.MaxPrecursorMass = #if $se_settings.SE_MaxPrecursorMass then $se_settings.SE_MaxPrecursorMass else 5000#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	118 SE.IsoPattern = #if $se_settings.SE_IsoPattern then $se_settings.SE_IsoPattern else 0.3#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	119 SE.MassDefectFilter = #if $se_settings.SE_MassDefectFilter then $se_settings.SE_MassDefectFilter else true#
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	120 SE.MassDefectOffset = #if $se_settings.SE_MassDefectOffset then $se_settings.SE_MassDefectOffset else 0.1#
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	121 #if $se_settings.SE_MinMS2NoPeakCluster:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	122 SE.MinMS2NoPeakCluster = $se_settings.SE_MinMS2NoPeakCluster
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	123 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	124 #if $se_settings.SE_MinRTRange:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	125 SE.MinRTRange = $se_settings.SE_MinRTRange
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	126 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	127 #if $se_settings.SE_RTtol:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	128 SE.RTtol = $se_settings.SE_RTtol
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	129 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	130 #if $se_settings.SE_Denoise:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	131 SE.Denoise = $se_settings.SE_Denoise
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	132 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	133 #if $se_settings.SE_NoPeakPerMin:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	134 SE.NoPeakPerMin = $se_settings.SE_NoPeakPerMin
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	135 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	136 #if $se_settings.SE_RemoveGroupedPeaks:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	137 SE.RemoveGroupedPeaks = $se_settings.SE_RemoveGroupedPeaks
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	138 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	139 #else:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	140 #Signal extraction parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	141 SE.SN = 2
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	142 SE.MS2SN = 2
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	143 SE.MinMSIntensity = 5
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	144 SE.MinMSMSIntensity = 1
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	145 SE.MaxCurveRTRange = 1
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	146 SE.NoMissedScan = 1
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	147 SE.MinFrag=10
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	148 SE.EstimateBG = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	149 SE.MinNoPeakCluster = 2
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	150 SE.MaxNoPeakCluster = 3#slurp
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	151 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	152
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	153 ## SE.RemoveGroupedPeaksRTOverlap
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	154 ## SE.RemoveGroupedPeaksCorr
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	155 ## SE.IsoCorrThreshold
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	156
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	157 #if $instrument.model != 'Thermo_Orbitrap':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	158 WindowType = $instrument.window.WindowType
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	159 #if $instrument.window.WindowType == 'SWATH':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	160 WindowSize = #if $instrument.window.WindowSize then $instrument.window.WindowSize else 25#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	161 #else if $instrument.window.WindowType == 'V_SWATH':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	162 ==window setting begin
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	163 #if $instrument.window.window_list.window_list_src == 'history':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	164 #set $fh = open(str($instrument.window.window_list.WindowListFile),'r')
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	165 #for $i,$line in enumerate($fh):
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	166 #set $fields = $line.split()
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	167 #if len($fields) >= 2:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	168 #set $win = '\t'.join($fields[:2])
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	169 $win
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	170 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	171 #end for
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	172 $fh.close()
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	173 #else:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	174 #set $win_list = $instrument.window.window_list.WindowList.split('\n')
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	175 #for $win in $win_list:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	176 #set $row = '\t'.join($win.split())
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	177 $row
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	178 #end for
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	179 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	180 ==window setting end
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	181 #echo '#'
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	182 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	183 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	184 #slurp]]>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	185 </configfile>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	186 </configfiles>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	187
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	188 <inputs>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	189 <param name="input" type="data" format="mzxml" label="Proteomics Spectrum files in mzXML format"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	190 <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of input">
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	191 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	192 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	193 <conditional name="instrument">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	194 <param name="model" type="select" label="instrument used" help="Sets default parameters">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	195 <option value="Thermo_Orbitrap">Thermo Orbitrap</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	196 <option value="AB_SCIEX_Triple_TOF_5600">AB SCIEX Triple TOF 5600</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	197 <option value="other">other</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	198 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	199 <when value="Thermo_Orbitrap">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	200 <param name="SE_MS1PPM" type="float" value="5" min="1" max="20" optional="true" label="Maximum mass error for two MS1 peaks">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	201 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	202 SE.MS1PPM: (Unit: ppm) Maximum mass error for two MS1 peaks in consecutive spectra to be considered signal of the same ion. Used in MS1 signal detection and precursor alignment between samples/runs.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	203 Recommended value: Depends on the instrument. Typical values are 5-10 ppm for Thermo Orbitrap.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	204 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	205 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	206 <param name="SE_MS2PPM" type="integer" value="5" min="1" max="20" optional="true" label="Maximum mass error for two MS2 peaks">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	207 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	208 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	209 Recommended value: Depends on the instrument. If fragmentation spectra are measured with the same detector as MS1 spectra, set the same as Para.MS1PPM or a little higher, e.g. if you've set Para.MS1PPM=30 ppm for AB SCIEX Triple TOF 5600, consider setting to 40ppm.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	210 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	211 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	212 <expand macro="common_se_params" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	213 </when>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	214 <when value="AB_SCIEX_Triple_TOF_5600">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	215 <param name="SE_MS1PPM" type="float" value="30" min="1" max="50" optional="true" label="Maximum mass error for two MS1 peaks">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	216 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	217 SE.MS1PPM: (Unit: ppm) Maximum mass error for two MS1 peaks in consecutive spectra to be considered signal of the same ion. Used in MS1 signal detection and precursor alignment between samples/runs.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	218 Recommended value: Depends on the instrument. Typical values are 20-40pm for AB SCIEX Triple TOF 5600.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	219 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	220 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	221 <param name="SE_MS2PPM" type="integer" value="40" min="1" max="50" optional="true" label="Maximum mass error for two MS2 peaks">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	222 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	223 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	224 Recommended value: Depends on the instrument. If fragmentation spectra are measured with the same detector as MS1 spectra, set the same as Para.MS1PPM or a little higher, e.g. if you've set Para.MS1PPM=30 ppm for AB SCIEX Triple TOF 5600, consider setting to 40ppm.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	225 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	226 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	227 <expand macro="common_se_params" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	228 <expand macro="se_window_params" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	229 </when>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	230 <when value="other">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	231 <param name="SE_MS1PPM" type="float" value="30" min="1" max="100" optional="true" label="Maximum mass error for two MS1 peaks">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	232 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	233 SE.MS1PPM: (Unit: ppm) Maximum mass error for two MS1 peaks in consecutive spectra to be considered signal of the same ion. Used in MS1 signal detection and precursor alignment between samples/runs.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	234 Recommended value: Depends on the instrument. Typical values are 5-10 ppm for Thermo Orbitrap, 20-40pm for AB SCIEX Triple TOF 5600.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	235 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	236 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	237 <param name="SE_MS2PPM" type="integer" value="40" min="1" max="100" optional="true" label="Maximum mass error for two MS2 peaks">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	238 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	239 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	240 Recommended value: Depends on the instrument. If fragmentation spectra are measured with the same detector as MS1 spectra, set the same as Para.MS1PPM or a little higher, e.g. if you've set Para.MS1PPM=30 ppm for AB SCIEX Triple TOF 5600, consider setting to 40ppm.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	241 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	242 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	243 <expand macro="common_se_params" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	244 <expand macro="se_window_params" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	245 </when>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	246 </conditional>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	247
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	248 <conditional name="frag_settings">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	249 <param name="advanced" type="select" label="Advanced Precursor-fragment Grouping Settings" help="Usually do not need to be changed">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	250 <option value="no">no</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	251 <option value="yes">yes</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	252 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	253 <when value="no"/>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	254 <when value="yes">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	255 <param name="RPmax" type="integer" value="25" optional="true" min="1" label="RPmax">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	256 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	257 RPmax: Determines how many precursors a single fragment is allowed to be grouped to. Precursors are first sorted by Pearson correlation of elution profiles; this option specifies the rank of a precursor in this sorted list. Lowering the value for this parameter increases the stringency of precursor-fragments grouping. (Default: 25)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	258 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	259 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	260 <param name="RFmax" type="integer" value="300" optional="true" min="1" label="RFmax">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	261 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	262 RFmax: Determines how many fragments a single precursor is allowed to have. Fragments are first sorted by Pearson correlation of elution profiles; this option specifies the rank of a fragment in this sorted list. The lower - the more stringent. (Default: 300)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	263 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	264 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	265 <param name="CorrThreshold" type="float" value=".2" optional="true" min="0." max="1." label="CorrThreshold">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	266 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	267 CorrThreshold: (0.0~1.0) Minimum Pearson correlation between a precursor and a fragment to be considered, the higher, the more stringent. (Default: 0.2)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	268 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	269 </param>
2 b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	270 <param name="RTOverlap" type="float" value=".3" min="0" optional="true" label="RTOverlap" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	271 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	272 RTOverlap: Retention time overlap. (Default: 0.3)
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	273 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	274 </param>
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	275 <param name="DeltaApex" type="float" value=".6" min="0" optional="true" label="DeltaApex" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	276 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	277 DeltaApex: (Unit: minute) Maximum retention time difference of LC profile apexes between precursor and fragment (the lower, the more stringent). (Default: 0.6)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	278 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	279 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	280 <param name="BoostComplementaryIon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="BoostComplementaryIon" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	281 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	282 BoostComplementaryIon: set to true if you want to boost complementary ions' intensity. The process of complementary ion boosting will also deisotope fragment peaks into singly charged m/z position. (Default: true)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	283 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	284 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	285 <param name="AdjustFragIntensity" type="boolean" truevalue="true" falsevalue="false" checked="true" label="AdjustFragIntensity" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	286 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	287 AdjustFragIntensity: set to true if you want to adjust fragment intensity by the Pearson correlation between a precursor and a fragment. (Default: true)
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	288 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	289 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	290 </when>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	291 </conditional>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	292
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	293 <conditional name="se_settings">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	294 <param name="advanced" type="select" label="Advanced Signal Extraction Settings" help="Usually do not need to be changed">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	295 <option value="no">no</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	296 <option value="yes">yes</option>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	297 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	298 <when value="no"/>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	299 <when value="yes">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	300 <param name="SE_MinMSIntensity" type="float" value="" optional="true" label="MinMSIntensity" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	301 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	302 SE.MinMSIntensity: Minimum signal intensity for a peak in an MS1 spectrum to be considered as a valid signal. Any MS1 peak having intensity lower than this threshold will be ignored. It is the main parameter controlling how many peaks and isotopic envelopes will be detected.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	303 Recommended value: Depends on the data. Check raw data for average noise- levels. E.g. TOF data often have thousands of random small intensity peaks.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	304 Warning: Setting this parameter too low (or zero) in such a case will significantly increase processing time and memory requirements.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	305 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	306 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	307 <param name="SE_MinMSMSIntensity" type="float" value="" optional="true" label="MinMSMSIntensity" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	308 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	309 SE.MinMSMSIntensity: Same as MinMSIntensity, but for MS2 signals.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	310 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	311 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	312 <param name="SE_MaxCurveRTRange" type="float" value="" optional="true" label="MaxCurveRTRange" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	313 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	314 SE.MaxCurveRTRange: (Unit: minute) The maximum allowed retention time (RT) range for elution profile of a single ion. If a detected elution profile exceeds that time span, it will be trimmed around the apex to fit into this range. Used to avoid having lots of ions which elute during the whole LC/MS run or over a very long period of time, as this greatly complicates grouping of precursors to fragments. Such long-eluting ions are likely to be contaminants, lock-mass ions, calibrants, etc.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	315 Recommended value: The expected maximum peak chromatographic time. E.g. set to several percent of the whole run time, if the run was 100 min long, set to 5 min.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	316 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	317 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	318 <param name="SE_SN" type="float" value="" optional="true" label="SN Threshold" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	319 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	320 SE.SN: Minimum signal-to-noise threshold for MS1 precursor signal detection. It is not the real S/N value, but rather a multiplier for MinMSIntensity, if a detected elution profile is less intense in the apex than SN x MinMSIntensity) it will be discarded.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	321 Recommended value: Typical values depend on the MinMSIntensity setting. If you've set MinMSIntensity to a very low value, consider setting this one to some small number in range 1.0 - 5.0.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	322 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	323 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	324 <param name="SE_MS2SN" type="float" value="" optional="true" label="MS2SN Threshold" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	325 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	326 Same as para.SN, but for possible unfragmented precursors in MS2 data (i.e. for selecting precursors to generate Q3 tier pseudo spectra).
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	327 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	328 </param>
2 b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	329 <param name="SE_StartRT" type="float" value="0" optional="true" label="StartRT" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	330 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	331 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	332 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	333 <param name="SE_EndRT" type="float" value="9999" optional="true" label="EndRT" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	334 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	335 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	336 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	337 <param name="SE_MinMZ" type="float" value="200" optional="true" label="MinMZ" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	338 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	339 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	340 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	341 <param name="SE_MinPrecursorMass" type="float" value="700" optional="true" label="MinPrecursorMass" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	342 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	343 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	344 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	345 <param name="SE_MaxPrecursorMass" type="float" value="5000" optional="true" label="MaxPrecursorMass" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	346 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	347 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	348 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	349 <param name="SE_IsoPattern" type="float" value="0.3" optional="true" label="IsoPattern" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	350 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	351 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	352 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	353 <param name="SE_MassDefectFilter" type="boolean" truevalue="true" falsevalue="false" checked="true" label="MassDefectFilter" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	354 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	355 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	356 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	357 <param name="SE_MassDefectOffset" type="float" value="0.1" optional="true" label="MassDefectOffset" >
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	358 <help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	359 </help>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	360 </param>
b4f82d15cac0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 6a5e8ce4711ed38bfb437a76d3a3d8dd8b322fed-dirty galaxyp parents: 1 diff changeset	361
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	362 <param name="SE_MinRTRange" type="float" value="" optional="true" label="MinRTRange" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	363 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	364 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	365 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	366 <param name="SE_MaxNoPeakCluster" type="integer" value="" optional="true" label="MaxNoPeakCluster" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	367 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	368 SE.MaxNoPeakCluster (new parameter in v1.4): Maximum number of isotope peaks for a precursor feature.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	369 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	370 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	371 <param name="SE_MinNoPeakCluster" type="integer" value="" optional="true" label="MinNoPeakCluster" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	372 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	373 SE.MinNoPeakCluster (new parameter in v1.4): Minimum number of isotope peaks for a precursor feature. When it is set as 1, the algorithm will group fragments even for peaks without any isotope signal being found. For these cases, the assumed charged states will be from the parameter SE.StartCharge to SE.EndCharge.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	374 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	375 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	376 <param name="SE_MinMS2NoPeakCluster" type="integer" value="" optional="true" label="MinMS2NoPeakCluster" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	377 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	378 SE.MinMS2NoPeakCluster (new parameter in v1.4): Minimum number of isotope peaks for a MS2 feature. When it is set as 1, the algorithm will group fragments even for peaks without any isotope signal being found. For these cases, the assumed charged states will be from the parameter SE.StartCharge to SE.EndCharge.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	379 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	380 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	381 <param name="SE_RTtol" type="float" value="" optional="true" label="RTtol" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	382 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	383 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	384 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	385 <param name="SE_NoPeakPerMin" type="integer" value="" optional="true" label="NoPeakPerMin" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	386 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	387 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	388 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	389 <param name="SE_NoMissedScan" type="integer" value="" optional="true" label="NoMissedScan" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	390 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	391 SE.NoMissedScan: Maximum number of consecutive "gaps" allowed during extraction of elution profile (scans, in which the precursor mass being traced was not detected). E.g. if set to 1 and a particular mass can be found at every second scan, the algorithm will trace such a peak unless it can't find the peak in 2 scans in a row.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	392 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	393 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	394 <param name="SE_Denoise" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Denoise" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	395 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	396 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	397 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	398 <param name="SE_EstimateBG" type="boolean" truevalue="true" falsevalue="false" checked="true" label="EstimateBG" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	399 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	400 SE.MinFrag: Minimum number of fragments for a precursor. Precursors which have less than the set number of fragments will be removed from pseudo MS/MS spectra.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	401 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	402 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	403 <param name="SE_RemoveGroupedPeaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="RemoveGroupedPeaks" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	404 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	405 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	406 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	407 <param name="SE_MinFrag" type="integer" value="" optional="true" label="MinFrag" >
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	408 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	409 SE.MinFrag: Minimum number of fragments for a precursor. Precursors which have less than the set number of fragments will be removed from pseudo MS/MS spectra.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	410 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	411 </param>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	412 </when>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	413 </conditional>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	414
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	415 <param name="ExportPrecursorPeak" type="boolean" truevalue="true" falsevalue="false" checked="false"
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	416 label="ExportPrecursorPeak"
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	417 help="Output detailed information about detected MS1 precursor and MS2 unfragmented precursor signals"/>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	418 <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false"
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	419 label="ExportFragmentPeak"
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	420 help="Output detailed information about detected MS2 signals"/>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	421 <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false"
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	422 label="Output MGFs as a collection" />
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	423
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	424 </inputs>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	425
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	426 <outputs>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	427 <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/>
4 e8822850243a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 3 diff changeset	428 <data format="txt" name="se_params" label="${tool.name} ${input.name} diaumpire_se.params"/>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	429 <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv">
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	430 <filter>ExportPrecursorPeak</filter>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	431 </data>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	432 <!--
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	433 <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	434 <filter>ExportFragmentPeak</filter>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	435 </data>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	436 -->
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	437 <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs">
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	438 <filter>mgfs_as_collection</filter>
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	439 <discover_datasets pattern="(?P<name>.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	440 </collection>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	441 <data format="mgf" name="q1_mgf" label="${tool.name} ${($input.name[:-6] if $input.name.endswith('.mxXML') or $input.name.endswith('.mxxml') else $input.name).rsplit('.',1)[0]}_Q1.mgf" >
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	442 <filter>not mgfs_as_collection</filter>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	443 </data>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	444 <data format="mgf" name="q2_mgf" label="${tool.name} ${($input.name[:-6] if $input.name.endswith('.mxXML') or $input.name.endswith('.mxxml') else $input.name).rsplit('.',1)[0]}_Q2.mgf" >
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	445 <filter>not mgfs_as_collection</filter>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	446 </data>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	447 <data format="mgf" name="q3_mgf" label="${tool.name} ${($input.name[:-6] if $input.name.endswith('.mxXML') or $input.name.endswith('.mxxml') else $input.name).rsplit('.',1)[0]}_Q3.mgf" >
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	448 <filter>not mgfs_as_collection</filter>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	449 </data>
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	450 </outputs>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	451 <tests>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	452 <test>
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	453 <param name="input" value="LongSwath_UPS1_1ug_rep1_xs.mzXML" ftype="mzxml"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	454 <conditional name="instrument">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	455 <param name="model" value="AB_SCIEX_Triple_TOF_5600"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	456 <param name="SE_MS1PPM" value="30"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	457 <param name="SE_MS2PPM" value="40"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	458 <conditional name="window">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	459 <param name="WindowType" value="SWATH"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	460 <param name="WindowSize" value="25"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	461 </conditional>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	462 </conditional>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	463 <output name="q2_mgf">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	464 <assert_contents>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	465 <has_text text="BEGIN IONS" />
4 e8822850243a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 3 diff changeset	466 <has_text text="PEPMASS=740" />
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	467 </assert_contents>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	468 </output>
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	469 </test>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	470 </tests>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	471 <help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	472 <![CDATA[
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	473 ================================
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	474 DIA-Umpire signal extraction
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	475 ================================
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	476
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	477 DIA_Umpire_SE.jar provides the signal extraction module for DIA data (regular SWATH with fixed isolation window size, variable window SWATH, MSX) which generates pseudo MS/MS spectra to be searched against a protein database using conventional proteomics search engines such as X!Tandem, SEQUEST, MSGF+, OMSSA, etc.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	478
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	479 Manual: http://sourceforge.net/projects/diaumpire/files/Manual/DIA_Umpire_Manual_v1.4_pre.pdf
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	480
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	481 Input (DIA-Umpire signal extraction module):
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	482 ================================================
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	483
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	484 1. Spectral data in mzXML format
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	485
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	486 Important: for AB SCIEX data, use AB SCIEX MS Data Converter (https://sciex.com/x32750):
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	487
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	488 Galaxy tool: https://toolshed.g2.bx.psu.edu/view/galaxyp/ms_data_converter/a36e9f847308
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	489
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	490 Use it for .wiff -> .mzML conversion, then use MSConvert for .mzML -> .mzXML. Read "Raw spectral data files conversion to mzXML" section in the manual for more details.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	491
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	492
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	493 Signal extraction parameters:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	494 =================================
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	495
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	496 SE.MS1PPM: (Unit: ppm) Maximum mass error for two MS1 peaks in consecutive spectra to be considered signal of the same ion. Used in MS1 signal detection and precursor alignment between samples/runs. Recommended value: Depends on the instrument. Typical values are 5-10 ppm for Thermo Orbitrap, 20-40pm for AB SCIEX Triple TOF 5600.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	497
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	498 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion. Recommended value: Depends on the instrument. If fragmentation spectra are measured with the same detector as MS1 spectra, set the same as Para.MS1PPM or a little higher, e.g. if you've set Para.MS1PPM=30 ppm for AB SCIEX Triple TOF 5600, consider setting to 40ppm.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	499
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	500 SE.Resolution: Used only if the input spectra are stored in profile mode (i.e. not centroided, e.g. by using "Peak Picking" option in MSConvert when converting raw spectral data to mzXML format). Profile spectra will be centroided using a sliding window. The window is moved across the entire mass range of a spectrum. Only the most intense peak in the window centered at the peak m/z is kept, others are discarded. The window width is calculated based on this parameter as: width = mz / para.Resolution. Recommended value: Depends on the instrument and acquisition settings. Either check raw data to see the real average resolution of peaks in spectra or consult vendor specifications for the instrument. For AB SCIEX TripleTOF 5600 we use 15000-20000.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	501
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	502 SE.StartCharge: The minimum charge state for MS1 precursor ion to be detected during isotopic peak grouping.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	503
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	504 SE.EndCharge: The maximum charge state for MS1 precursor ion to be detected during isotopic peak grouping. Recommended value: it is not recommended to set this parameter higher than 5 for typical proteomic experiments, as it is unlikely to observe peptides of higher charge states.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	505
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	506 SE.MS2StartCharge: The minimum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	507
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	508 SE.MS2EndCharge: The maximum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping. Recommended value: it is not recommended to set this parameter higher than 5 for typical proteomic experiments, as it is unlikely to observe peptides of higher charge states.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	509
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	510 DIA isolation window settings:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	511
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	512 WindowType: DIA experiment type. DIA is implemented differently by different vendors and current support for data-formats is lacking, so the program needs additional info to properly interpret input spectral data. Supported values in this version:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	513
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	514 * SWATH - fixed window size SWATH, as described in the original SWATH paper. If you're using this option, it's mandatory to specify WindowSize option as well.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	515
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	516 * V_SWATH - variable window size SWATH. If you're using this option, it's mandatory to specify Variable SWATH window setting (see section below).
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	517
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	518 * MSX - 2Da isolation window, its position is shuffled randomly until the whole MS1 range is covered, the process is then repeated but coverage of MS1 range by isolation windows will be different because of randomization.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	519
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	520 * MSE - as originally implemented in Waters instruments. The full MS1 range is being fragmented at once.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	521
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	522 WindowSize: Isolation window size setting for fixed window SWATH. (Please skip this part if the data is from Thermo instrument) Note: The window size is to be specified including overlapping regions. I.e. if your windows are: 399.5-425.5, 424.5 - 450.5, etc., then the window size should be set to 26. Note: Was tested only on AB SCIEX TripleTOF 5600 and Thermo Q-Exactive and Fusion data.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	523
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	524 Variable SWATH window setting: Isolation settings for variable window size SWATH. (Please skip this part if the data is from Thermo instrument). The format should be a tab-delimited list of m/z low and high values, one window per row.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	525
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	526
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	527 Output files of DIA-Umpire signal extraction module:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	528 ========================================================
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	529
3 6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 2 diff changeset	530 1. DIA_Umpire_SE MGFs - Three .mgf files per input .mzXML file - pseudo MS/MS spectra sets for different quality categories of detected precursor signals (see the Online Methods of the publication for details). These can be either individual history items or a dataset collection. Example:
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	531
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	532 1. <filename>_Q1.mgf
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	533 2. <filename>_Q2.mgf
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	534 3. <filename>_Q3.mgf
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	535
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	536 Note: Each file corresponds to a different "quality level" of precursor ions (Q1= More than two isotopic peaks detected in MS1, Q2 = only two isotopic peak detected, Q3 = detected unfragmented precursor in MS2). These spectra are written to separate files, because they must be searched separately against a protein database as a consequence of differences in FDR estimates for these varying quality data.
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	537
4 e8822850243a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f galaxyp parents: 3 diff changeset	538 2. If ExportPrecursorPeak and/or ExportFragmentPeak options were set to true, text files with detailed information about detected MS1 and/or MS2 features will be generated.
0 e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	539
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	540
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	541 ]]>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	542 </help>
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	543 <expand macro="citations" />
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8 galaxyp parents: diff changeset	544 </tool>

Mercurial > repos > galaxyp > dia_umpire

annotate dia_umpire_se.xml @ 4:e8822850243a draft default tip