Mercurial > repos > galaxyp > proteomiqon_mzmltomzlite

annotate proteomiqon_mzmltomzlite.xml @ 0:529b61ba3d64 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
author galaxyp
date Wed, 30 Jun 2021 16:31:24 +0000
parents
children acb8aba959ed
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0
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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1 <tool id="proteomiqon_mzmltomzlite" name="ProteomIQon MzMLToMzLite" version="@VERSION@" python_template_version="20.05">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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2 <description>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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3 converts mzML files to mzLite files.
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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4 </description>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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5 <macros>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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6 <token name="@VERSION@">0.0.5</token>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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7 </macros>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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8 <requirements>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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9 <requirement type="package" version="@VERSION@">proteomiqon-mzmltomzlite</requirement>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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10 </requirements>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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11 <command detect_errors="exit_code"><![CDATA[
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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12 #import re
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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13 #set basename = $re.sub(r'[^\w ,.\-+]','_',$instrumentOutput.element_identifier)
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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14 #if $outputParamfile:
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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15 cat '$paramfile' >> '$out_paramfile' &&
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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16 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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17 ln -s $instrumentOutput '${basename}.mzML' &&
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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18 ln -s $out_mzlite '${basename}.mzlite' &&
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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19 proteomiqon-mzmltomzlite -i './${basename}.mzML' -p $paramfile -o ./
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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20 ]]>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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21 </command>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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22 <configfiles>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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23 <configfile name="paramfile">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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24 <![CDATA[
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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25 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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26 "Compress":${BinaryDataCompressionType},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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27 #if $StartRetentionTime
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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28 "StartRetentionTime":
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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29 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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30 "Case" : "Some",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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31 "Fields" : [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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32 ${StartRetentionTime}
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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33 ],
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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34 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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35
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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36 #else
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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37 "StartRetentionTime":null,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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38 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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39 #if $EndRetentionTime
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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40 "EndRetentionTime":
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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41 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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42 "Case" : "Some",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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43 "Fields" : [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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44 ${EndRetentionTime}
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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45 ],
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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46 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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47 #else
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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48 "EndRetentionTime":null,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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49 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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50 "MS1PeakPicking": {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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51 "Case": "${Ms1PeakPickingCond.Ms1PeakPicking}",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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52 #if $Ms1PeakPickingCond.Ms1PeakPicking == "Centroid"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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53 "Fields" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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54 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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55 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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56 "Case" : "${Ms1PeakPickingCond.CentroidModeCond.CentroidMode}",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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57 #if $Ms1PeakPickingCond.CentroidModeCond.CentroidMode == "Wavelet"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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58 "Fields" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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59 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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60 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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61 "NumberOfScales" : ${Ms1PeakPickingCond.CentroidModeCond.NumberOfScales},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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62 "YThreshold" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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63 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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64 "Case" : "${Ms1PeakPickingCond.CentroidModeCond.YThresholdCond.YThreshold}",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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65 #if $Ms1PeakPickingCond.CentroidModeCond.YThresholdCond.YThreshold == "Fixed"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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66 "Fields":
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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67 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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68 ${Ms1PeakPickingCond.CentroidModeCond.YThresholdCond.Ms1YThreshold},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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69 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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70 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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71 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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72 "Centroid_MzTolerance" : ${Ms1PeakPickingCond.CentroidModeCond.Centroid_MzTolerance},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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73 "SNRS_Percentile" : ${Ms1PeakPickingCond.CentroidModeCond.SNRS_Percentile},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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74 "MinSNR" : ${Ms1PeakPickingCond.CentroidModeCond.MinSNR},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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75 "RefineMZ" : ${Ms1PeakPickingCond.CentroidModeCond.RefineMZ},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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76 "SumIntensities" : ${Ms1PeakPickingCond.CentroidModeCond.SumIntensities},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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77 #if $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.usePaddingparams == "yes"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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78 "PaddingParams" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
79 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
80 "Case" : "Some",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
81 "Fields" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
82 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
83 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
84 #if $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.MaximumPaddingPointsCond.specifyMaximumPaddingPoints == "yes"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
85 "MaximumPaddingPoints" : {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
86 "Case" : "Some",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
87 "Fields" : [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
88 $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.MaximumPaddingPointsCond.MaximumPaddingPoints
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
89 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
90 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
91 #else
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
92 "MaximumPaddingPoints" : null,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
93 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
94 "Padding_MzTolerance" : $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.Padding_MzTolerance,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
95 "WindowSize" : $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.WindowSize,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
96 "SpacingPerc" : $Ms1PeakPickingCond.CentroidModeCond.PaddingParamsCond.SpacingPerc
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
97 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
98 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
99
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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diff changeset
100 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
101 #else
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
102 "PaddingParams" : null
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
103 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
104 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
105
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
106 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
107 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
108 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
109 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
110 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
111 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
112 "MS2PeakPicking": {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
113 "Case": "${Ms2PeakPickingCond.Ms2PeakPicking}",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
114 #if $Ms2PeakPickingCond.Ms2PeakPicking == "Centroid"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
115 "Fields" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
116 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
117 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
118 "Case" : "${Ms2PeakPickingCond.CentroidModeCond.CentroidMode}",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
119 #if $Ms2PeakPickingCond.CentroidModeCond.CentroidMode == "Wavelet"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
120 "Fields" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
121 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
122 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
123 "NumberOfScales" : ${Ms2PeakPickingCond.CentroidModeCond.NumberOfScales},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
124 "YThreshold" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
125 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
126 "Case" : "${Ms2PeakPickingCond.CentroidModeCond.YThresholdCond.YThreshold}",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
127 #if $Ms2PeakPickingCond.CentroidModeCond.YThresholdCond.YThreshold == "Fixed"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
128 "Fields":
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
129 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
130 ${Ms2PeakPickingCond.CentroidModeCond.YThresholdCond.Ms2YThreshold},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
131 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
132 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
133 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
134 "Centroid_MzTolerance" : ${Ms2PeakPickingCond.CentroidModeCond.Centroid_MzTolerance},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
135 "SNRS_Percentile" : ${Ms2PeakPickingCond.CentroidModeCond.SNRS_Percentile},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
136 "MinSNR" : ${Ms2PeakPickingCond.CentroidModeCond.MinSNR},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
137 "RefineMZ" : ${Ms2PeakPickingCond.CentroidModeCond.RefineMZ},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
138 "SumIntensities" : ${Ms2PeakPickingCond.CentroidModeCond.SumIntensities},
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
139 #if $Ms2PeakPickingCond.CentroidModeCond.PaddingParamsCond.usePaddingparams == "yes"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
140 "PaddingParams" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
141 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
142 "Case" : "Some",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
143 "Fields" :
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
144 [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
145 {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
146 #if $Ms2PeakPickingCond.CentroidModeCond.PaddingParamsCond.MaximumPaddingPointsCond.specifyMaximumPaddingPoints == "yes"
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
147 "MaximumPaddingPoints" : {
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
148 "Case" : "Some",
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
149 "Fields" : [
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
150 $Ms2PeakPickingCond.CentroidModeCond.PaddingParamsCond.MaximumPaddingPointsCond.MaximumPaddingPoints
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
151 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
152 },
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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diff changeset
153 #else
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
154 "MaximumPaddingPoints" : null,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
155 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
156 "Padding_MzTolerance" : $Ms2PeakPickingCond.CentroidModeCond.PaddingParamsCond.Padding_MzTolerance,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
157 "WindowSize" : $Ms2PeakPickingCond.CentroidModeCond.PaddingParamsCond.WindowSize,
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
158 "SpacingPerc" : $Ms2PeakPickingCond.CentroidModeCond.PaddingParamsCond.SpacingPerc
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
159 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
160 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
161
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
162 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
163 #else
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
164 "PaddingParams" : null
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
165 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
166 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
167
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
168 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
169 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
170 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
171 ]
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
172 #end if
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
173 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
174 }
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
175 ]]>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
176 </configfile>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
177 </configfiles>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
178 <inputs>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
179 <param name="instrumentOutput" type="data" format="mzml" label="Instrument output" help="Please specify the .mzML file you want to convert"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
180 <param name="BinaryDataCompressionType" type="select" label="Binary data compression type">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
181 <option value="0" selected="true">No compression</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
182 <option value="1">ZLib</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
183 <option value="2">Num press</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
184 <option value="3">Num press ZLib</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
185 <option value="4">Num press Pic</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
186 <option value="5">Num press Lin</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
187 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
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diff changeset
188 <param name="StartRetentionTime" type="float" optional="true" label="Start retention time" help="You can optionally specify a minimum scan time. MS scans measured earlier will not be copied."/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
189 <param name="EndRetentionTime" type="float" optional="true" label="End retention time" help="You can optionally specify a maximum scan time. MS scans measured at a later scan time will not be copied."/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
190 <conditional name="Ms1PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
191 <param name="Ms1PeakPicking" type="select" label="MS1 peak picking">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
192 <option value="ProfilePeaks" selected="true">Profile peaks</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
193 <option value="Centroid">Centroid</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
194 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
195 <when value="Centroid">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
196 <conditional name="CentroidModeCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
197 <param name="CentroidMode" type="select" label="Centroidization mode">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
198 <option value="Manufacturer">Manufacturer</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
199 <option value="Wavelet">Wavelet</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
200 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
201 <when value="Wavelet">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
202 <param name="NumberOfScales" type="integer" value="0" label="Number of scales"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
203 <conditional name="YThresholdCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
204 <param name="YThreshold" type="select" label="Y threshold">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
205 <option value="Fixed" selected="true">Fixed</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
206 <option value="MinSpectrumIntensity">Min spectrum intensity</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
207 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
208 <when value="Fixed">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
209 <param name="Ms1YThreshold" type="float" value="0" label="Value"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
210 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
211 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
212 <param name="Centroid_MzTolerance" type="float" value="0" label="Centroid MZ tolerance"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
213 <param name="SNRS_Percentile" type="float" value="0" label="SNRS percentile"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
214 <param name="MinSNR" type="float" value="0" label="Min SNR"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
215 <param name="RefineMZ" type="boolean" value="false" label="Refine MZ"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
216 <param name="SumIntensities" type="boolean" value="false" label="Sum intensities"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
217 <conditional name="PaddingParamsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
218 <param name="usePaddingparams" type="select" checked="false" label="Specify padding parameters">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
219 <option value="yes">Yes</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
220 <option value="no">No</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
221 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
222 <when value="yes">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
223 <conditional name="MaximumPaddingPointsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
224 <param name="specifyMaximumPaddingPoints" type="select" label="Speficy maximum padding points">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
225 <option value="yes">Yes</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
226 <option value="no">No</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
227 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
228 <when value="yes">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
229 <param name="MaximumPaddingPoints" type="integer" value="0" label="Maximum padding points"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
230 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
231 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
232 <param name="Padding_MzTolerance" type="float" value="0" label="Padding MZ tolerance"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
233 <param name="WindowSize" type="integer" value="0" label="Window size"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
234 <param name="SpacingPerc" type="float" value="0" label="Spacing perc"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
235 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
236 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
237 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
238 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
239 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
240 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
241 <conditional name="Ms2PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
242 <param name="Ms2PeakPicking" type="select" label="MS2 peak picking">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
243 <option value="ProfilePeaks" selected="true">Profile peaks</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
244 <option value="Centroid">Centroid</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
245 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
246 <when value="Centroid">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
247 <conditional name="CentroidModeCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
248 <param name="CentroidMode" type="select" label="Centroidization mode">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
249 <option value="Manufacturer">Manufacturer</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
250 <option value="Wavelet">Wavelet</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
251 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
252 <when value="Wavelet">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
253 <param name="NumberOfScales" type="integer" value="0" label="Number of scales"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
254 <conditional name="YThresholdCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
255 <param name="YThreshold" type="select" label="Y threshold">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
256 <option value="Fixed" selected="true">Fixed</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
257 <option value="MinSpectrumIntensity">Min spectrum intensity</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
258 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
259 <when value="Fixed">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
260 <param name="Ms2YThreshold" type="float" value="0" label="Value"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
261 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
262 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
263 <param name="Centroid_MzTolerance" type="float" value="0" label="Centroid MZ tolerance"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
264 <param name="SNRS_Percentile" type="float" value="0" label="SNRS percentile"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
265 <param name="MinSNR" type="float" value="0" label="Min SNR"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
266 <param name="RefineMZ" type="boolean" value="false" label="Refine MZ"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
267 <param name="SumIntensities" type="boolean" value="false" label="Sum intensities"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
268 <conditional name="PaddingParamsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
269 <param name="usePaddingparams" type="select" label="Specify padding parameters">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
270 <option value="yes">Yes</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
271 <option value="no">No</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
272 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
273 <when value="yes">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
274 <conditional name="MaximumPaddingPointsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
275 <param name="specifyMaximumPaddingPoints" type="select" label="Speficy maximum padding points">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
276 <option value="yes">Yes</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
277 <option value="no">No</option>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
278 </param>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
279 <when value="yes">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
280 <param name="MaximumPaddingPoints" type="integer" value="0" label="Maximum padding points"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
281 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
282 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
283 <param name="Padding_MzTolerance" type="float" value="0" label="Padding MZ tolerance"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
284 <param name="WindowSize" type="integer" value="0" label="Window size"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
285 <param name="SpacingPerc" type="float" value="0" label="Spacing perc"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
286 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
287 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
288 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
289 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
290 </when>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
291 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
292 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
293 </inputs>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
294 <outputs>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
295 <data format="sqlite" name="out_mzlite" />
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
296 <data format="json" name="out_paramfile">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
297 <filter>outputParamfile</filter>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
298 </data>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
299 </outputs>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
300 <tests>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
301 <test expect_num_outputs="2">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
302 <param name="instrumentOutput" value="sample.mzml"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
303 <param name="BinaryDataCompressionType" value="0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
304 <param name="StartRetentionTime" value=""/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
305 <param name="EndRetentionTime" value=""/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
306 <conditional name="Ms1PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
307 <param name="Ms1PeakPicking" value="ProfilePeaks"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
308 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
309 <conditional name="Ms2PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
310 <param name="Ms2PeakPicking" value="ProfilePeaks"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
311 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
312 <param name="outputParamfile" value="true"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
313 <output name="out_paramfile" file="result_1.json"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
314 </test>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
315 <test expect_num_outputs="2">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
316 <param name="instrumentOutput" value="sample.mzml"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
317 <param name="BinaryDataCompressionType" value="0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
318 <param name="StartRetentionTime" value=""/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
319 <param name="EndRetentionTime" value=""/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
320 <conditional name="Ms1PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
321 <param name="Ms1PeakPicking" value="Centroid"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
322 <conditional name="CentroidModeCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
323 <param name="CentroidMode" value="Wavelet"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
324 <param name="NumberOfScales" value="3"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
325 <conditional name="YThresholdCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
326 <param name="YThreshold" value="Fixed"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
327 <param name="Ms1YThreshold" value="1"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
328 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
329 <param name="Centroid_MzTolerance" value="0.1"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
330 <param name="SNRS_Percentile" value="95.0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
331 <param name="MinSNR" value="1.0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
332 <param name="RefineMZ" value="false"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
333 <param name="SumIntensities" value="false"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
334 <conditional name="PaddingParamsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
335 <param name="usePaddingparams" value="no"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
336 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
337 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
338 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
339 <conditional name="Ms2PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
340 <param name="Ms2PeakPicking" value="ProfilePeaks"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
341 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
342 <param name="outputParamfile" value="true"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
343 <output name="out_paramfile" file="result_2.json"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
344 </test>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
345 <test expect_num_outputs="2">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
346 <param name="instrumentOutput" value="sample.mzml"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
347 <param name="BinaryDataCompressionType" value="0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
348 <param name="StartRetentionTime" value=""/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
349 <param name="EndRetentionTime" value=""/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
350 <conditional name="Ms1PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
351 <param name="Ms1PeakPicking" value="ProfilePeaks"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
352 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
353 <conditional name="Ms2PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
354 <param name="Ms2PeakPicking" value="Centroid"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
355 <conditional name="CentroidModeCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
356 <param name="CentroidMode" value="Wavelet"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
357 <param name="NumberOfScales" value="10"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
358 <conditional name="YThresholdCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
359 <param name="YThreshold" value="MinSpectrumIntensity"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
360 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
361 <param name="Centroid_MzTolerance" value="0.1"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
362 <param name="SNRS_Percentile" value="95.0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
363 <param name="MinSNR" value="1.0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
364 <param name="RefineMZ" value="false"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
365 <param name="SumIntensities" value="false"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
366 <conditional name="PaddingParamsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
367 <param name="usePaddingparams" value="yes"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
368 <conditional name="MaximumPaddingPointsCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
369 <param name="specifyMaximumPaddingPoints" value="yes" />
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
370 <param name="MaximumPaddingPoints" value="7" />
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
371 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
372 <param name="Padding_MzTolerance" value="0.005" />
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
373 <param name="WindowSize" value="150"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
374 <param name="SpacingPerc" value="95"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
375 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
376 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
377 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
378 <param name="outputParamfile" value="true"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
379 <output name="out_paramfile" file="result_3.json"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
380 </test>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
381 <test expect_num_outputs="2">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
382 <param name="instrumentOutput" value="sample.mzml"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
383 <param name="BinaryDataCompressionType" value="0"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
384 <param name="StartRetentionTime" value="6.75"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
385 <param name="EndRetentionTime" value="6.75"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
386 <conditional name="Ms1PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
387 <param name="Ms1PeakPicking" value="ProfilePeaks"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
388 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
389 <conditional name="Ms2PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
390 <param name="Ms2PeakPicking" value="ProfilePeaks"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
391 </conditional>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
392 <param name="outputParamfile" value="true"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
393 <output name="out_paramfile" file="result_4.json"/>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
394 </test>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
galaxyp
parents:
diff changeset
395 <test expect_num_outputs="1">
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396 <param name="instrumentOutput" value="sample.mzml"/>
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397 <param name="BinaryDataCompressionType" value="0"/>
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398 <param name="StartRetentionTime" value="6.75"/>
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399 <param name="EndRetentionTime" value="6.75"/>
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400 <conditional name="Ms1PeakPickingCond">
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401 <param name="Ms1PeakPicking" value="ProfilePeaks"/>
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402 </conditional>
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403 <conditional name="Ms2PeakPickingCond">
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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404 <param name="Ms2PeakPicking" value="ProfilePeaks"/>
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405 </conditional>
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406 </test>
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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407 </tests>
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408 <help>
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409 <![CDATA[
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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410 Introduction
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411 ------------
529b61ba3d64 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite commit adc8b0dc45ba060c7c82ab3df028141339956475"
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412 The success of modern proteomics was made possible by constant progression in the field of mass spectrometry.
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413 Over the course of the past years quite a few manufacturers of mass spectrometers have managed to establish themselfes in the field of biological research.
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414 Since aquisition and accession of mass spectra are performance critical processes, various performance optimized, but vendor specific and closed source formats have been developed to store raw MS data.
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415 This comes to the disadvantage for toolchain developers which want to provide tools for every scientist regardless of the format of their raw data.
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416
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417 In a effort to provide an open format for the storage of MS data the format mzML was developed. While this XML based format is straight forward to implement it falls behind in performance critical scenarios.
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418 To be competitive in performance and to comply to the FAIR principles we chose to use mzLite, an open and SQLite based implementation of mzML, within our toolchain.
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419
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420 What It Does
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421 ------------
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422 The tool mzMLToMzLite allows to convert mzML files to mzLite files. Additionally, it allows the user to perform peak picking or filtering of mass spectra.
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423 We recommend the use of `_msconvert <https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2>`_ to convert your raw data into .mzML.
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424
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425 Further Reading
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426 ---------------
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427 Additional information about the tool can be found in the `_documentation <https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html>`_.
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428 ]]>
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429 </help>
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430 </tool>