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annotate dia_umpire_se.xml @ 1:acd0df26c1e9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 73496bb9686e60f25d1cccf3410f1c53bf92d5f5-dirty
author galaxyp
date Wed, 24 Jan 2018 08:08:58 -0500
parents e8f7be6a6e59
children b4f82d15cac0
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e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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1 <tool id="dia_umpire_se" name="DIA_Umpire_SE" version="@VERSION@.0">
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2 <description>DIA signal extraction</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 #import re
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11 ## want to save all outputs in a directory output.extra_files_path to be used by dia_umpire_quant
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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12 ## Is file naming going to be a problem? May need to have a name param
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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13 #if $se_extraction_data:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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14 #set $ser_dir = $se_params.extra_files_path
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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15 mkdir $ser_dir
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16 && ln -s '$ser_dir' '$output_dir'
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17 #else:
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18 mkdir '$output_dir'
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19 #end if
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20 && cat $se_config > $se_params
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21 ##
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22 && echo " " >> $se_params
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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23 && echo "Thread = \$GALAXY_SLOTS" >> $se_params
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24 #if $input_prefix and len($input_prefix.strip()) > 0:
1
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25 #set $input_path = str($output_dir) + '/' + $input_prefix.__str__ + '_rep' + str($i + 1) + '.mzXML'
0
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26 #else:
1
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27 #set $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + '.mzXML'
0
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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28 #end if
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29 && ln -s '${input}' '$input_path'
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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30 && dia_umpire_se '$input_path' '$se_params'
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31 && cat $output_dir/*.log >> "$logfile"
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32 #if not $mgfs_as_collection:
1
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33 && cp "$output_dir/"*_Q1.mgf '$q1_mgf'
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34 && cp "$output_dir/"*_Q2.mgf '$q2_mgf'
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35 && cp "$output_dir/"*_Q3.mgf '$q3_mgf'
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36 #end if
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37 #if $ExportPrecursorPeak:
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38 && cp "$output_dir/"*PeakCluster.csv '$PrecursorPeak'
0
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39 #end if
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40 ]]>
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41 </command>
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42 <configfiles>
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43 <configfile name="se_config"><![CDATA[#slurp
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44 #DIA-Umpire (version @VERSION@)
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45 #Data Independent Acquisition data processing and analysis package (Signal extraction module)
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46
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47 #import re
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48 #if $input_prefix:
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49 #set $input_path = $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML"
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50 #else:
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51 #set $input_path = $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + ".mzXML"
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52 #end if
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53 # $input.name $input_path $input
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54
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55 #No of threads
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56 Thread = 6
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57
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58 #Report peak
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59 ExportPrecursorPeak = $ExportPrecursorPeak
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60 ExportFragmentPeak = $ExportFragmentPeak
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61
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62 #Signal extraction parameters
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63 #if $instrument.model == 'Thermo_Orbitrap':
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64 SE.MS1PPM = #if $instrument.SE_MS1PPM then $instrument.SE_MS1PPM else 5#
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65 SE.MS2PPM = #if $instrument.SE_MS2PPM then $instrument.SE_MS2PPM else 5#
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66 SE.Resolution = #if $instrument.SE_Resolution then $instrument.SE_Resolution else 17000#
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67 SE.StartCharge = #if $instrument.SE_StartCharge then $instrument.SE_StartCharge else 2#
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68 SE.EndCharge = #if $instrument.SE_EndCharge then $instrument.SE_EndCharge else 4#
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69 SE.MS2StartCharge = #if $instrument.SE_MS2StartCharge then $instrument.SE_MS2StartCharge else 2#
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70 SE.MS2EndCharge = #if $instrument.SE_MS2EndCharge then $instrument.SE_MS2EndCharge else 4#
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71 #else if $instrument.model == 'AB_SCIEX_Triple_TOF_5600':
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72 SE.MS1PPM = #if $instrument.SE_MS1PPM then $instrument.SE_MS1PPM else 30#
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73 SE.MS2PPM = #if $instrument.SE_MS2PPM then $instrument.SE_MS2PPM else 40#
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74 SE.Resolution = #if $instrument.SE_Resolution then $instrument.SE_Resolution else 17000#
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75 SE.StartCharge = #if $instrument.SE_StartCharge then $instrument.SE_StartCharge else 2#
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76 SE.EndCharge = #if $instrument.SE_EndCharge then $instrument.SE_EndCharge else 4#
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77 SE.MS2StartCharge = #if $instrument.SE_MS2StartCharge then $instrument.SE_MS2StartCharge else 2#
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78 SE.MS2EndCharge = #if $instrument.SE_MS2EndCharge then $instrument.SE_MS2EndCharge else 4#
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79 #else:
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80 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
81 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
82 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
83 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
84 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
85 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
86 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
87 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
parents:
diff changeset
88
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
89 #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
90 #Fragment grouping parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
91 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
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diff changeset
92 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
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diff changeset
93 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
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diff changeset
94 DeltaApex = #if $frag_settings.DeltaApex then $frag_settings.DeltaApex else 0.6#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
95 RTOverlap = 0.3
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
96 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
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diff changeset
97 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
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98 #else:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
99 #Fragment grouping parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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100 RPmax = 25
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
101 RFmax = 300
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
102 CorrThreshold = 0.2
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
103 DeltaApex = 0.6
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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104 AdjustFragIntensity = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
105 BoostComplementaryIon = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
106 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
107
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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108 #if $se_settings.advanced == 'yes':
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
109 #Signal extraction parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
110 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
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diff changeset
111 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
112 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
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diff changeset
113 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
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diff changeset
114 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
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diff changeset
115 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
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116 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
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diff changeset
117 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
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diff changeset
118 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
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diff changeset
119 SE.MaxNoPeakCluster = #if $se_settings.SE_MaxNoPeakCluster then $se_settings.SE_MaxNoPeakCluster else 4#
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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120 SE.StartRT = 0
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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121 SE.EndRT = 9999
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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122 SE.MinMZ = 200
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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123 SE.MinPrecursorMass = 700
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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124 SE.MaxPrecursorMass = 5000
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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125 SE.IsoPattern = 0.3
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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126 SE.MassDefectFilter = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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127 SE.MassDefectOffset = 0.1
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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128 #if $se_settings.SE_MinMS2NoPeakCluster:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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129 SE.MinMS2NoPeakCluster = $se_settings.SE_MinMS2NoPeakCluster
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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130 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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131 #if $se_settings.SE_MinRTRange:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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132 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
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diff changeset
133 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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134 #if $se_settings.SE_RTtol:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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135 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
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diff changeset
136 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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137 #if $se_settings.SE_Denoise:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
138 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
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diff changeset
139 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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140 #if $se_settings.SE_NoPeakPerMin:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
141 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
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diff changeset
142 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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143 #if $se_settings.SE_RemoveGroupedPeaks:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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144 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
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diff changeset
145 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
146 #else:
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
147 #Signal extraction parameters
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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148 SE.SN = 2
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galaxyp
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149 SE.MS2SN = 2
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galaxyp
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diff changeset
150 SE.MinMSIntensity = 5
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
151 SE.MinMSMSIntensity = 1
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
152 SE.MaxCurveRTRange = 1
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galaxyp
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153 SE.NoMissedScan = 1
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
154 SE.MinFrag=10
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galaxyp
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diff changeset
155 SE.EstimateBG = true
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
156 SE.MinNoPeakCluster = 2
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
157 SE.MaxNoPeakCluster = 3#slurp
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
158 #end if
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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diff changeset
159
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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160 ## SE.RemoveGroupedPeaksRTOverlap
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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161 ## SE.RemoveGroupedPeaksCorr
e8f7be6a6e59 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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162 ## SE.IsoCorrThreshold
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163
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164 #if $instrument.model != 'Thermo_Orbitrap':
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165 WindowType = $instrument.window.WindowType
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166 #if $instrument.window.WindowType == 'SWATH':
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167 WindowSize = #if $instrument.window.WindowSize then $instrument.window.WindowSize else 25#
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168 #else if $instrument.window.WindowType == 'V_SWATH':
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169 ==window setting begin
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170 #if $instrument.window.window_list.window_list_src == 'history':
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171 #set $fh = open(str($instrument.window.window_list.WindowListFile),'r')
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172 #for $i,$line in enumerate($fh):
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173 #set $fields = $line.split()
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174 #if len($fields) >= 2:
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175 #set $win = '\t'.join($fields[:2])
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176 $win
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177 #end if
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178 #end for
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179 $fh.close()
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180 #else:
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181 #set $win_list = $instrument.window.window_list.WindowList.split('\n')
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182 #for $win in $win_list:
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183 #set $row = '\t'.join($win.split())
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184 $row
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185 #end for
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186 #end if
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187 ==window setting end
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188 #echo '#'
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189 #end if
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190 #end if
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191 #slurp]]>
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192 </configfile>
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193 </configfiles>
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194
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195 <inputs>
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196 <param name="input" type="data" format="mzxml" label="Proteomics Spectrum files in mzXML format"/>
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197 <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">
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198 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
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199 </param>
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200 <param name="output_dir" type="hidden" value="gx_path"/>
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201
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202 <conditional name="instrument">
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203 <param name="model" type="select" label="instrument used" help="Sets default parameters">
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204 <option value="Thermo_Orbitrap">Thermo Orbitrap</option>
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205 <option value="AB_SCIEX_Triple_TOF_5600">AB SCIEX Triple TOF 5600</option>
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206 <option value="other">other</option>
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207 </param>
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208 <when value="Thermo_Orbitrap">
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209
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210 <param name="SE_MS1PPM" type="float" value="5" min="1" max="20" optional="true" label="Maximum mass error for two MS1 peaks">
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211 <help>
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212 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.
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213 Recommended value: Depends on the instrument. Typical values are 5-10 ppm for Thermo Orbitrap.
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214 </help>
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215 </param>
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216 <param name="SE_MS2PPM" type="integer" value="5" min="1" max="20" optional="true" label="Maximum mass error for two MS2 peaks">
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217 <help>
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218 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion.
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219 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
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220 </help>
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221 </param>
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222 <expand macro="common_se_params" />
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223
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224 </when>
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225 <when value="AB_SCIEX_Triple_TOF_5600">
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226 <param name="SE_MS1PPM" type="float" value="30" min="1" max="50" optional="true" label="Maximum mass error for two MS1 peaks">
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227 <help>
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228 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.
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229 Recommended value: Depends on the instrument. Typical values are 20-40pm for AB SCIEX Triple TOF 5600.
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230 </help>
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231 </param>
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232 <param name="SE_MS2PPM" type="integer" value="40" min="1" max="50" optional="true" label="Maximum mass error for two MS2 peaks">
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233 <help>
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234 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion.
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235 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
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236 </help>
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237 </param>
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238 <expand macro="common_se_params" />
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239 <expand macro="se_window_params" />
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240 </when>
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241 <when value="other">
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242 <param name="SE_MS1PPM" type="float" value="30" min="1" max="100" optional="true" label="Maximum mass error for two MS1 peaks">
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243 <help>
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244 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.
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245 Recommended value: Depends on the instrument. Typical values are 5-10 ppm for Thermo Orbitrap, 20-40pm for AB SCIEX Triple TOF 5600.
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246 </help>
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247 </param>
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248 <param name="SE_MS2PPM" type="integer" value="40" min="1" max="100" optional="true" label="Maximum mass error for two MS2 peaks">
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249 <help>
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250 SE.MS2PPM: (Unit: ppm) Maximum mass error for two MS2 peaks in consecutive spectra to be considered signal of the same ion.
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251 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.
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252 </help>
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253 </param>
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254 <expand macro="common_se_params" />
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255 <expand macro="se_window_params" />
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256 </when>
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257 </conditional>
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258
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259 <conditional name="frag_settings">
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260 <param name="advanced" type="select" label="Advanced Precursor-fragment Grouping Settings" help="Usually do not need to be changed">
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261 <option value="no">no</option>
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262 <option value="yes">yes</option>
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263 </param>
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264 <when value="no"/>
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265 <when value="yes">
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266 <param name="RPmax" type="integer" value="25" optional="true" min="1" label="RPmax">
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267 <help>
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268 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)
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269 </help>
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270 </param>
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271 <param name="RFmax" type="integer" value="300" optional="true" min="1" label="RFmax">
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272 <help>
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273 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)
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274 </help>
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275 </param>
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276 <param name="CorrThreshold" type="float" value=".2" optional="true" min="0." max="1." label="CorrThreshold">
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277 <help>
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278 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)
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279 </help>
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280 </param>
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281
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282 <param name="DeltaApex" type="float" value=".6" min="0" optional="true" label="DeltaApex" >
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283 <help>
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284 DeltaApex: (Unit: minute) Maximum retention time difference of LC profile apexes between precursor and fragment (the lower, the more stringent). (Default: 0.6)
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285 </help>
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286 </param>
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287 <param name="BoostComplementaryIon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="BoostComplementaryIon" >
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288 <help>
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289 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)
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290 </help>
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291 </param>
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292 <param name="AdjustFragIntensity" type="boolean" truevalue="true" falsevalue="false" checked="true" label="AdjustFragIntensity" >
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293 <help>
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294 AdjustFragIntensity: set to true if you want to adjust fragment intensity by the Pearson correlation between a precursor and a fragment. (Default: true)
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295 </help>
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296 </param>
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297 </when>
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298 </conditional>
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299
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300 <conditional name="se_settings">
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301 <param name="advanced" type="select" label="Advanced Signal Extraction Settings" help="Usually do not need to be changed">
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302 <option value="no">no</option>
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303 <option value="yes">yes</option>
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304 </param>
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305 <when value="no"/>
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306 <when value="yes">
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307
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308 <param name="SE_MinMSIntensity" type="float" value="" optional="true" label="MinMSIntensity" >
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309 <help>
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310 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.
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311 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.
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312 Warning: Setting this parameter too low (or zero) in such a case will significantly increase processing time and memory requirements.
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313 </help>
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314 </param>
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315 <param name="SE_MinMSMSIntensity" type="float" value="" optional="true" label="MinMSMSIntensity" >
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316 <help>
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317 SE.MinMSMSIntensity: Same as MinMSIntensity, but for MS2 signals.
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318 </help>
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319 </param>
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320 <param name="SE_MaxCurveRTRange" type="float" value="" optional="true" label="MaxCurveRTRange" >
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321 <help>
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322 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.
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323 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.
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324 </help>
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325 </param>
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326 <param name="SE_SN" type="float" value="" optional="true" label="SN Threshold" >
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327 <help>
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328 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
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329 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.
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330 </help>
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331 </param>
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332 <param name="SE_MS2SN" type="float" value="" optional="true" label="MS2SN Threshold" >
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333 <help>
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334 Same as para.SN, but for possible unfragmented precursors in MS2 data (i.e. for selecting precursors to generate Q3 tier pseudo spectra).
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335 </help>
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336 </param>
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337 <param name="SE_MinRTRange" type="float" value="" optional="true" label="MinRTRange" >
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338 <help>
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339
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340 </help>
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341 </param>
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342 <param name="SE_MaxNoPeakCluster" type="integer" value="" optional="true" label="MaxNoPeakCluster" >
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343 <help>
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344 SE.MaxNoPeakCluster (new parameter in v1.4): Maximum number of isotope peaks for a precursor feature.
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345 </help>
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346 </param>
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347 <param name="SE_MinNoPeakCluster" type="integer" value="" optional="true" label="MinNoPeakCluster" >
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348 <help>
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349 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.
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350 </help>
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351 </param>
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352 <param name="SE_MinMS2NoPeakCluster" type="integer" value="" optional="true" label="MinMS2NoPeakCluster" >
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353 <help>
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354 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.
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355
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356 </help>
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357 </param>
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358 <param name="SE_RTtol" type="float" value="" optional="true" label="RTtol" >
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359 <help>
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360 </help>
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361 </param>
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362 <param name="SE_NoPeakPerMin" type="integer" value="" optional="true" label="NoPeakPerMin" >
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363 <help>
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364 </help>
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365 </param>
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366 <param name="SE_NoMissedScan" type="integer" value="" optional="true" label="NoMissedScan" >
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367 <help>
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368 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.
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369 </help>
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370 </param>
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371 <param name="SE_Denoise" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Denoise" >
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372 <help>
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373 </help>
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374 </param>
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375 <param name="SE_EstimateBG" type="boolean" truevalue="true" falsevalue="false" checked="true" label="EstimateBG" >
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376 <help>
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377 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.
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378 </help>
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379 </param>
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380 <param name="SE_RemoveGroupedPeaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="RemoveGroupedPeaks" >
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381 <help>
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382 </help>
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383 </param>
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384 <param name="SE_MinFrag" type="integer" value="" optional="true" label="MinFrag" >
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385 <help>
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386 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.
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387 </help>
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388 </param>
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389 </when>
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390 </conditional>
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391
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392 <param name="ExportPrecursorPeak" type="boolean" truevalue="true" falsevalue="false" checked="false"
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393 label="ExportPrecursorPeak"
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394 help="Output detailed information about detected MS1 precursor and MS2 unfragmented precursor signals"/>
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395 <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false"
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396 label="ExportFragmentPeak"
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397 help="Output detailed information about detected MS2 signals"/>
1
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398 <param name="se_extraction_data" type="boolean" truevalue="Signal Extraction data" falsevalue="diaumpire_se.params" checked="false"
0
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399 label="Output Signal Extraction data for DIA_Umpire_Quant" />
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400 <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false"
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401 label="Output MGFs as a collection" />
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402
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403 </inputs>
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404
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405 <outputs>
1
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406 <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/>
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407 <data format="dia_umpire.ser" name="se_params" label="${tool.name} ${input.name} ${se_extraction_data}">
0
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408 </data>
1
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409 <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv">
0
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410 <filter>ExportPrecursorPeak</filter>
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411 </data>
1
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412 <!--
0
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413 <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
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414 <filter>ExportFragmentPeak</filter>
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415 </data>
1
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416 -->
0
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417 <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs">
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418 <filter>mgfs_as_collection</filter>
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419 <discover_datasets pattern="(?P&lt;name&gt;.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" />
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420 </collection>
1
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421 <data format="mgf" name="q1_mgf" label="${tool.name} ${input.name}_Q1.mgf" >
0
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422 <filter>not mgfs_as_collection</filter>
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423 </data>
1
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424 <data format="mgf" name="q2_mgf" label="${tool.name} ${input.name}_Q2.mgf" >
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425 <filter>not mgfs_as_collection</filter>
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426 </data>
1
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427 <data format="mgf" name="q3_mgf" label="${tool.name} ${input.name}_Q3.mgf" >
0
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428 <filter>not mgfs_as_collection</filter>
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429 </data>
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430 </outputs>
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431 <tests>
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432 <test>
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433 <param name="input" value="LongSwath_UPS1_1ug_rep1_xs.mzXML" ftype="mzxml"/>
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434 <output name="q2_mgf" file="LongSwath_UPS1_1ug_rep1_xs_Q2.mgf"/>
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435 </test>
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436 </tests>
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437 <help>
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438 <![CDATA[
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439 ================================
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440 **DIA-Umpire signal extraction**
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441 ================================
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442
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443 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.
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444
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445 Manual: http://sourceforge.net/projects/diaumpire/files/Manual/DIA_Umpire_Manual_v1.4_pre.pdf
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446
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447 **Input** (DIA-Umpire signal extraction module):
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448 ================================================
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449
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450 1. Spectral data in mzXML format
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451
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452 **Important**: for AB SCIEX data, use AB SCIEX MS Data Converter (http://goo.gl/wf7KRV):
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453 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.
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454
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455 **Signal extraction parameters**:
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456 =================================
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457
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458 *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.
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459
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460 *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.
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461
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462 *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.
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463
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464 *SE.StartCharge*: The minimum charge state for MS1 precursor ion to be detected during isotopic peak grouping.
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465
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466 *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.
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467
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468 *SE.MS2StartCharge*: The minimum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping.
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469
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470 *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.
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471
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472 **DIA isolation window settings**:
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473
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474 *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:
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475
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476 * 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.
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477
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478 * V_SWATH - variable window size SWATH. If you're using this option, it's mandatory to specify Variable SWATH window setting (see section below).
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479
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480 * 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.
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481
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482 * MSE - as originally implemented in Waters instruments. The full MS1 range is being fragmented at once.
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483
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484 *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.
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485
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486 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.
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487
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488
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489 **Output files of DIA-Umpire signal extraction module**:
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490 ========================================================
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491
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492 1. *DIA_Umpire_SE MGFs* - A Dataset Collection containing 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). Example:
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493
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494 1. <filename>_Q1.mgf
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495 2. <filename>_Q2.mgf
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496 3. <filename>_Q3.mgf
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497
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498 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.
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499
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500 2. *DIA_Umpire_SE Signal Extraction data* - includes the binary files (.ser) containing contain all necessary information for quantitation procedures (parameter settings, all detected precursor and fragment peaks, precursor-fragment grouping information).
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501
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502 3. 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.
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503
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504
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505 ]]>
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506 </help>
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507 <expand macro="citations" />
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508 </tool>