spectrast: spectrast_search.xml annotate

annotate spectrast_search.xml @ 5:274fdc50169b draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty

author	jjohnson
date	Wed, 25 Jul 2018 15:05:34 -0400
parents	7f02fc51bddf
children

rev	line source
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	1 <tool id="specrast_search" name="SpectraST Search" version="@VERSION@.0">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	2 <description>with Spectral Library</description>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	3 <macros>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	4 <import>macros.xml</import>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	5 </macros>
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	6 <expand macro="requirements">
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	7 </expand>
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	9 ## Need to symlink to data using name with extension that spectrast recognizes
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	10 #import re
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	11 ## spectrum datasets
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	12 #set global $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'msp': 'msp', 'mzdata':'mzData'}
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	13 #set global $input_files = []
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	14 #def ln_scan($sf):
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	15 #set $ext = '.' + $exts[$sf.extension.lower()]
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	16 #set $input_name = $re.sub('[.]([^.]*)$',$ext,$sf.display_name.split('/')[-1])
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	17 #silent $input_files.append($input_name)
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	18 ln -s -f '${sf}' '${input_name}' &&
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	19 #set $encoded_id = $__app__.security.encode_id($sf.id)
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	20 echo "Spectrums:${sf.display_name}(API:${encoded_id}) ";
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	21 #end def
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	22 #if $collection.collection_selector == 'dataset':
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	23 $ln_scan($collection.spectrum_file)
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	24 #else:
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	25 #for $spectrum_file in $collection.spectrum_files:
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	26 $ln_scan($spectrum_file)
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	27 #end for
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	28 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	29 python $__tool_directory__/spectrast_params.py
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 2 diff changeset	30 --mode=search
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	31 #if $spectrastParams:
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	32 '$spectrastParams'
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	33 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	34 '$spectrast_params' -o spectrast.params &&
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	35 mkdir out &&
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	36 spectrast -sFspectrast.params -sL'${libraryFile.extra_files_path}/library.splib' -sO out -sE $outputExtension
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	37 #echo ' '.join($input_files)
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	38 && ls -l out
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	39 #if $collection.collection_selector == 'dataset':
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	40 && cp out/* $output
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	41 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	42 ]]></command>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	43 <configfiles>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	44 <configfile name="spectrast_params"><![CDATA[#slurp
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	45 libraryFile = ${libraryFile.extra_files_path}/library.splib
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	46 #if str($general.databaseFile) != 'None':
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	47 databaseFile = $general.databaseFile
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	48 #if $general.databaseType is not None:
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	49 databaseType = $general.databaseType
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	50 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	51 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	52 #if $general.indexCacheAll is not None:
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	53 indexCacheAll = $general.indexCacheAll
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	54 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	55 ## #if $filterSelectedListFileName is not None:
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	56 ## filterSelectedListFileName = $filterSelectedListFileName
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	57 ## #end if
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	58 #if $candidate_selection_and_scoring.precursorMzTolerance is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	59 precursorMzTolerance = $candidate_selection_and_scoring.precursorMzTolerance
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	60 #end if
3 7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty jjohnson parents: 2 diff changeset	61 #eif str($candidate_selection_and_scoring.precursorMzUseAverage) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	62 precursorMzUseAverage = $candidate_selection_and_scoring.precursorMzUseAverage
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	63 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	64 #if str($candidate_selection_and_scoring.searchAllCharges) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	65 searchAllCharges = $candidate_selection_and_scoring.searchAllCharges
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	66 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	67 #if $candidate_selection_and_scoring.detectHomologs is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	68 detectHomologs = $candidate_selection_and_scoring.detectHomologs
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	69 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	70 #if $candidate_selection_and_scoring.fvalFractionDelta is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	71 fvalFractionDelta = $candidate_selection_and_scoring.fvalFractionDelta
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	72 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	73 #if str($candidate_selection_and_scoring.useSp4Scoring) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	74 useSp4Scoring = $candidate_selection_and_scoring.useSp4Scoring
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	75 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	76 #if str($candidate_selection_and_scoring.fvalUseDotBias) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	77 fvalUseDotBias = $candidate_selection_and_scoring.fvalUseDotBias
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	78 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	79 #if str($candidate_selection_and_scoring.usePValue) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	80 usePValue = $candidate_selection_and_scoring.usePValue
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	81 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	82 #if str($candidate_selection_and_scoring.useTierwiseOpenModSearch) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	83 useTierwiseOpenModSearch = $candidate_selection_and_scoring.useTierwiseOpenModSearch
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	84 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	85 #if $outputExtension is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	86 outputExtension = $outputExtension
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	87 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	88 ## #if $outputDirectory is not None:
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	89 ## outputDirectory = $outputDirectory
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	90 ## #end if
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	91 #if $output_and_display.hitListTopHitFvalThreshold is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	92 hitListTopHitFvalThreshold = $output_and_display.hitListTopHitFvalThreshold
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	93 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	94 #if $output_and_display.hitListLowerHitsFvalThreshold is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	95 hitListLowerHitsFvalThreshold = $output_and_display.hitListLowerHitsFvalThreshold
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	96 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	97 #if str($output_and_display.hitListShowHomologs) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	98 hitListShowHomologs = $output_and_display.hitListShowHomologs
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	99 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	100 #if $output_and_display.hitListShowMaxRank is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	101 hitListShowMaxRank = $output_and_display.hitListShowMaxRank
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	102 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	103 #if str($output_and_display.hitListOnlyTopHit) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	104 hitListOnlyTopHit = $output_and_display.hitListOnlyTopHit
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	105 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	106 #if str($output_and_display.hitListExcludeNoMatch) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	107 hitListExcludeNoMatch = $output_and_display.hitListExcludeNoMatch
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	108 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	109 #if $output_and_display.enzymeForPepXMLOutput is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	110 enzymeForPepXMLOutput = $output_and_display.enzymeForPepXMLOutput
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	111 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	112 #if str($printFingerprintingSummary) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	113 printFingerprintingSummary = $printFingerprintingSummary
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	114 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	115 #if $spectrum_filtering.filterMinPeakCount is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	116 filterMinPeakCount = $spectrum_filtering.filterMinPeakCount
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	117 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	118 #if $spectrum_filtering.filterAllPeaksBelowMz is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	119 filterAllPeaksBelowMz = $spectrum_filtering.filterAllPeaksBelowMz
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	120 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	121 #if $spectrum_filtering.filterMaxIntensityBelow is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	122 filterMaxIntensityBelow = $spectrum_filtering.filterMaxIntensityBelow
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	123 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	124 #if $spectrum_filtering.filterMinMzRange is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	125 filterMinMzRange = $spectrum_filtering.filterMinMzRange
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	126 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	127 #if $spectrum_filtering.filterCountPeakIntensityThreshold is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	128 filterCountPeakIntensityThreshold = $spectrum_filtering.filterCountPeakIntensityThreshold
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	129 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	130 #if $spectrum_processing.filterRemovePeakIntensityThreshold is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	131 filterRemovePeakIntensityThreshold = $spectrum_processing.filterRemovePeakIntensityThreshold
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	132 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	133 #if $spectrum_processing.filterMaxPeaksUsed is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	134 filterMaxPeaksUsed = $spectrum_processing.filterMaxPeaksUsed
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	135 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	136 #if $spectrum_processing.filterMaxDynamicRange is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	137 filterMaxDynamicRange = $spectrum_processing.filterMaxDynamicRange
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	138 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	139 #if $spectrum_processing.peakScalingMzPower is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	140 peakScalingMzPower = $spectrum_processing.peakScalingMzPower
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	141 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	142 #if $spectrum_processing.peakScalingIntensityPower is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	143 peakScalingIntensityPower = $spectrum_processing.peakScalingIntensityPower
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	144 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	145 #if $spectrum_processing.peakScalingUnassignedPeaks is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	146 peakScalingUnassignedPeaks = $spectrum_processing.peakScalingUnassignedPeaks
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	147 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	148 #if str($spectrum_processing.peakNoBinning) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	149 peakNoBinning = $spectrum_processing.peakNoBinning
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	150 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	151 #if $spectrum_processing.peakBinningNumBinsPerMzUnit is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	152 peakBinningNumBinsPerMzUnit = $spectrum_processing.peakBinningNumBinsPerMzUnit
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	153 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	154 #if $spectrum_processing.peakBinningFractionToNeighbor is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	155 peakBinningFractionToNeighbor = $spectrum_processing.peakBinningFractionToNeighbor
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	156 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	157 #if $spectrum_processing.filterLibMaxPeaksUsed is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	158 filterLibMaxPeaksUsed = $spectrum_processing.filterLibMaxPeaksUsed
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	159 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	160 #if $spectrum_processing.filterLightIonsMzThreshold is not None:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	161 filterLightIonsMzThreshold = $spectrum_processing.filterLightIonsMzThreshold
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	162 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	163 #if str($spectrum_processing.filterITRAQReporterPeaks) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	164 filterITRAQReporterPeaks = $spectrum_processing.filterITRAQReporterPeaks
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	165 #end if
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	166 #if str($spectrum_processing.filterTMTReporterPeaks) != 'None':
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	167 filterTMTReporterPeaks = $spectrum_processing.filterTMTReporterPeaks
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	168 #end if
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	169 ]]>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	170 </configfile>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	171 </configfiles>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	172 <inputs>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	173 <conditional name="collection">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	174 <param name="collection_selector" type="select" label="Process Spectrums Indivdiual or Collection ">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	175 <option value="dataset" selected="true">Search Single Spectrum file and output results as a dataset</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	176 <option value="collection">Search Multiple Spectrum files and output results as a collection</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	177 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	178 <when value="dataset">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	179 <param name="spectrum_file" type="data" format="mzxml,mzml,mgf,msp,mzdata" label="Spectrum file" help="mzxml,mzml,mgf,msp,mzdata"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	180 </when>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	181 <when value="collection">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	182 <param name="spectrum_files" multiple="true" type="data" format="mzxml,mzml,mgf,msp,mzdata" label="Spectrum files" help="mzxml,mzml,mgf,msp,mzdata"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	183 </when>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	184 </conditional>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	185
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	186 <param name="libraryFile" type="data" format="splib" label="Spectral library" help=""/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	187 <param name="spectrastParams" type="data" format="txt" optional="true" label="SpectraST param file" help=""/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	188 <section name="general" expanded="false" title="General Options">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	189 <param name="databaseFile" type="data" format="fasta" label="Fasta sequence database" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	190 help="will not affect the search in any way, but this information will be included in the output for any downstream data processing."/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	191 <param name="databaseType" type="select" label="Database type: Protein or DNA" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	192 <option value="AA" selected="true">protein AA</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	193 <option value="DNA">genomic DNA</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	194 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	195 <param name="indexCacheAll" type="boolean" label="indexCacheAll" help="Cache all entries in RAM. Requires a lot of memory (the library will usually be loaded almost in its entirety), but speeds up search for unsorted queries."/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	196 </section>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	197 <section name="candidate_selection_and_scoring" expanded="false" title="Candidate Selection and Scoring Options">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	198 <param name="precursorMzTolerance" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	199 label="precursorMzTolerance"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	200 help="Specify precursor m/z tolerance in Th. Monoisotopic mass is assumed. Default is 3.0"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	201 <param name="precursorMzUseAverage" type="select" optional="true" label="precursorMzUseAverage Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	202 <help> Report average mass instead of monoisotopic mass in search results.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	203 Precursor m/z window is expanded to account for difference between average and monoisotopic mass.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	204 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	205 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	206 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	207 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	208 <param name="searchAllCharges" type="select" optional="true" label="searchAllCharges Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	209 <help> Report average mass instead of monoisotopic mass in search results.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	210 Precursor m/z window is expanded to account for difference between average and monoisotopic mass.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	211 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	212 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	213 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	214 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	215 <param name="detectHomologs" type="integer" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	216 label="detectHomologs"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	217 help="Detect homologous lower hits up to this rank. Looks for lower hits homologous to the top hit and adjust delta accordingly. Default is 4"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	218 <param name="fvalFractionDelta" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	219 label="fvalFractionDelta"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	220 help="Specify the fraction of the normalized delta score (delta/dot) in the F-value formula. Default is 0.4"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	221 <param name="useSp4Scoring" type="select" optional="true" label="useSp4Scoring (SP4) Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	222 <help> Use original SpectraST (4.0 or earlier) scoring, based on dot products of square-root intensities.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	223 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	224 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	225 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	226 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	227 <param name="fvalUseDotBias" type="select" optional="true" label="fvalUseDotBias (Only applicable for SP4 scoring) Default: true" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	228 <help> Use dot bias to penalize high-scoring matches with massive noise and/or dominant peak.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	229 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	230 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	231 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	232 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	233 <param name="usePValue" type="select" optional="true" label="usePValue (NOT applicable for SP4 scoring) Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	234 <help> Use dot bias to penalize high-scoring matches with massive noise and/or dominant peak.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	235 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	236 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	237 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	238 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	239 <param name="useTierwiseOpenModSearch" type="select" optional="true" label="useTierwiseOpenModSearch (NOT applicable for SP4 scoring) Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	240 <help> Perform tier-wise open modification search for modifications within precursor m/z window specified.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	241 Note that the scoring is different from normal SpectraST searches.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	242 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	243 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	244 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	245 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	246 </section>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	247 <section name="output_and_display" expanded="false" title="Output and Display Options">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	248 <param name="hitListTopHitFvalThreshold" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	249 label="hitListTopHitFvalThreshold"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	250 help="Minimum F value threshold for the top hit. Only top hits having F value greater than this will be printed. Default is 0.0 (all top hits)"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	251 <param name="hitListLowerHitsFvalThreshold" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	252 label="hitListLowerHitsFvalThreshold"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	253 help="Minimum F value threshold for the lower hits. Only lower hits having F value greater than this will be printed. Default=0.45"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	254 <param name="hitListShowHomologs" type="select" optional="true" label="hitListShowHomologs Default: true" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	255 <help> Always displays homologous lower hits regardless of F value.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	256 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	257 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	258 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	259 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	260 <param name="hitListShowMaxRank" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	261 label="hitListShowMaxRank"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	262 help="Maximum rank for hits shown for each query. Default is 1 (Just the top hit)"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	263 <param name="hitListOnlyTopHit" type="select" optional="true" label="hitListOnlyTopHit Default: true" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	264 <help> Only display the top hit for each query.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	265 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	266 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	267 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	268 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	269 <param name="hitListExcludeNoMatch" type="select" optional="true" label="hitListExcludeNoMatch Default: true" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	270 <help> Do not display queries for which there is no candidate, or the top hit is below the minimum F value threshold specified.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	271 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	272 <option value="true">true</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	273 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	274 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	275 <param name="enzymeForPepXMLOutput" type="text" value="trypsin" optional="true" label="enzymeForPepXMLOutput">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	276 <help>Specify the proteolytic enzyme used, for the purpose of pepXML output.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	277 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	278 <option value="trypsin">trypsin</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	279 <option value="lysc">lysc</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	280 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	281 </section>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	282 <section name="spectrum_filtering" expanded="false" title="Spectrum Filtering Options">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	283 <param name="filterMinPeakCount" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	284 label="filterMinPeakCount"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	285 help="Discard query spectra with fewer than peaks above set threshold. Default is 10"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	286 <param name="filterAllPeaksBelowMz" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	287 label="filterAllPeaksBelowMz"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	288 help="Discard query spectra with almost no peaks above specified m/z value. All query spectra with 95%+ of the total intensity below m/z will be removed. Default is 520"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	289 <param name="filterMaxIntensityBelow" type="integer" value="" optional="true" min="0"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	290 label="filterMinPeakCount"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	291 help="Discard query spectra with no peaks with intensity above this. Default is 0"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	292 <param name="filterMinMzRange" type="integer" value="" optional="true" min="0"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	293 label="filterMinMzRange"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	294 help="Discard query spectra with m/z range narrower than this. Default 350"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	295 <param name="filterCountPeakIntensityThreshold" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	296 label="filterCountPeakIntensityThreshold"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	297 help="Minimum peak intensity for peaks to be counted. Only peaks with intensity above this will be counted to meet the requirement for minimum number of peaks. Default is 2.01"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	298 </section>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	299 <section name="spectrum_processing" expanded="false" title="Spectrum Processing Options">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	300 <param name="filterRemovePeakIntensityThreshold" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	301 label="filterRemovePeakIntensityThreshold"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	302 help="Noise peak threshold. All peaks with intensities below this will be zeroed. Default is 2.01"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	303 <param name="filterMaxPeaksUsed" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	304 label="filterMaxPeaksUsed"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	305 help="Remove all but the top number peaks in query spectra. Default 150"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	306 <param name="filterMaxDynamicRange" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	307 label="filterMaxDynamicRange"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	308 help="Remove all peaks smaller than 1/number of the base (highest) peak in query spectra. Default 1000"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	309
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	310 <param name="peakScalingMzPower" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	311 label="peakScalingMzPower"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	312 help="Intensity scaling power with respect to the m/z value and the raw intensity. The scaled intensity will be (m/z)^mzpow * (raw intensity)^intpow Default is 2.01"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	313 <param name="peakScalingIntensityPower" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	314 label="peakScalingIntensityPower"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	315 help="Intensity scaling power with respect to the m/z value and the raw intensity. The scaled intensity will be (m/z)^mzpow * (raw intensity)^intpow Default is 2.01"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	316
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	317 <param name="peakScalingUnassignedPeaks" type="float" value="" optional="true" min="0.0"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	318 label="peakScalingUnassignedPeaks"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	319 help="Scaling factor for unassigned peaks in library spectra. Default is 1.0"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	320 <param name="peakNoBinning" type="select" optional="true" label="peakNoBinning Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	321 <help> Only display the top hit for each query.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	322 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	323 <option value="true">true - Disable binning and perform peak-to-peak matching.</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	324 <option value="false">false - Use binning</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	325 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	326 <param name="peakBinningNumBinsPerMzUnit" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	327 label="peakBinningNumBinsPerMzUnit"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	328 help="Number of bins per Th. Default 1"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	329 <param name="peakBinningFractionToNeighbor" type="float" value="" optional="true"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	330 label="peakBinningFractionToNeighbor"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	331 help="Fraction of the scaled intensity assigned to neighboring bins. Default is 0.5"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	332 <param name="filterLibMaxPeaksUsed" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	333 label="filterLibMaxPeaksUsed"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	334 help="Remove all but the top peaks in the LIBRARY spectra. Default 50"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	335 <param name="filterLightIonsMzThreshold" type="integer" value="" optional="true" min="1"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	336 label="filterLightIonsMzThreshold"
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	337 help="Remove all light ions with m/z lower than this Th for both library and query spectra. Default 180"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	338 <param name="filterITRAQReporterPeaks" type="select" optional="true" label="filterITRAQReporterPeaks Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	339 <help> Remove iTRAQ reporter peaks in the range 112-122 Th.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	340 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	341 <option value="true">true - Remove iTRAQ reporter peaks</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	342 <option value="false">false - Use binning</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	343 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	344 <param name="filterTMTReporterPeaks" type="select" optional="true" label="filterTMTReporterPeaks Default: false" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	345 <help> Remove TMT reporter peaks in the range 126-132 Th.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	346 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	347 <option value="true">true - Remove TMT reporter peaks</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	348 <option value="false">false</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	349 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	350 </section>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	351
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	352 <param name="outputExtension" type="select" label="Output format">
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	353 <option value="pep.xml">pep.xml</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	354 <option value="xls">xls (tabular)</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	355 <option value="txt">txt (fixed width text)</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	356 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	357 <param name="printFingerprintingSummary" type="select" optional="true" label="printFingerprintingSummary Default: no" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	358 <help> Print a text file summarizing fingerprinting results.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	359 </help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	360 <option value="fingerprint.summary">yes</option>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	361 </param>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	362 </inputs>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	363 <outputs>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	364 <data name="log" format="txt" label="spectrast.log" from_work_dir="spectrast.log"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	365 <data name="params" format="txt" label="spectrast.params" from_work_dir="spectrast.params"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	366 <data name="fingerprint_summary" format="txt" label="fingerprint.summary" from_work_dir="fingerprint.summary">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	367 <filter>printFingerprintingSummary and printFingerprintingSummary == 'fingerprint.summary'</filter>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	368 </data>
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	369 <data name="output" format="pepxml" label="${tool.name} on ${on_string}: ${outputExtension}">
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	370 <filter>collection['collection_selector'] == 'dataset'</filter>
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	371 <change_format>
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	372 <when input="outputExtension" value="xls" format="tabular" />
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	373 <when input="outputExtension" value="txt" format="txt" />
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	374 </change_format>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	375 <actions>
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	376 <conditional name="outputExtension">
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	377 <when value="xls">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	378 <action name="column_names" type="metadata" default="Geneid,${','.join([a.name for a in $input_files])}" />
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	379 </when>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	380 </conditional>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	381 </actions>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	382 </data>
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	383 <collection name="output_pepxml" type="list" label="${tool.name} on ${on_string}: ${outputExtension} collection">
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	384 <filter>collection['collection_selector'] == 'collection' and outputExtension == 'pep.xml'</filter>
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	385 <discover_datasets pattern="(?P<designation>.+\.pep.xml)" ext="pepxml" directory="out" visible="false" />
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	386 </collection>
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	387 <collection name="output_xls" type="list" label="${tool.name} on ${on_string}: ${outputExtension} collection">
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	388 <filter>collection['collection_selector'] == 'collection' and outputExtension == 'xls'</filter>
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	389 <discover_datasets pattern="(?P<designation>.+\.xls)" ext="tabular" directory="out" visible="false" />
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	390 </collection>
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	391 <collection name="output_txt" type="list" label="${tool.name} on ${on_string}: ${outputExtension} collection">
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	392 <filter>collection['collection_selector'] == 'collection' and outputExtension == 'txt'</filter>
e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	393 <discover_datasets pattern="(?P<designation>.+\.txt)" ext="txt" directory="out" visible="false" />
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	394 </collection>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	395 </outputs>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	396 <tests>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	397 <test>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	398 <param name="spectrum_files" value="msgf-test.mzML" ftype="mzml" />
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	399 <param name="libraryFile" value="splib.html" ftype="splib" >
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	400 <composite_data value="splib/library.splib"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	401 <composite_data value="splib/library.spidx"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	402 <composite_data value="splib/library.pepidx"/>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	403 </param>
2 e67b0cc10377 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit af2d54a900c86c6b9926b87b514517c0f0f0a975-dirty jjohnson parents: 1 diff changeset	404 <param name="outputExtension" value="xls"/>
1 390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	405 <output name="output">
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	406 <assert_contents>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	407 <has_text text="FKWNGTDTNSAAEK" />
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	408 </assert_contents>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	409 </output>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	410 </test>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	411 </tests>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	412 <help><![CDATA[
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	413 SpectraST Search
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	414
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	415 SpectraST_ can perform spectral searching from the following data formats:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	416
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	417 .mzML format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	418 .mzXML (all versions) format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	419 .mzData format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	420 .mgf (Mascot Generic) format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	421 .dta (SEQUEST) format, a simple peak list preceded by precursor information
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	422 NIST (National Institute of Standards and Technology)'s .msp format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	423
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	424 The spectral library must be in SpectraST's .splib format,
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	425 which can be created in SpectraST Create
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	426 or imported from .msp format which can be generated by BiblioSpec_.
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	427
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	428 The results can be outputted to the following formats:
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	429 .pepXML format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	430 .txt format, a fixed-width column text format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	431 .xls format, a tab-delimited column text format
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	432
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	433 .. _SpectraST: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#SpectraST_Create_Mode
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	434 .. _BiblioSpec: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=default
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	435
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	436 ]]></help>
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	437 <expand macro="citations" />
390a3c4a7f6b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 301559f22171a8644b5be6cefc2a26cd477b6a7f-dirty jjohnson parents: diff changeset	438 </tool>

Mercurial > repos > jjohnson > spectrast

annotate spectrast_search.xml @ 5:274fdc50169b draft default tip