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comparison encyclopedia_walnut.xml @ 5:4936de9f9024 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:39:11 -0400
parents 2f36eba0b877
children 0172dfa08216
comparison
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4:2f36eba0b877 5:4936de9f9024
59 <actions> 59 <actions>
60 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 60 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
61 </actions> 61 </actions>
62 </data> 62 </data>
63 </outputs> 63 </outputs>
64 <tests>
65 <test>
66 <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/>
67 <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/>
68 <output name="features" ftype="tabular">
69 <assert_contents>
70 <has_text text="LHYNEGLNIK"/>
71 </assert_contents>
72 </output>
73 </test>
74 </tests>
64 <help><![CDATA[ 75 <help><![CDATA[
76
77 <help><![CDATA[
78
79 **Walnut**
80
81 @ENCYCLOPEDIA_WIKI@
82
65 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data. 83 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
66 Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides. 84 Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.
67 85
68 Required Parameters:
69 -i input .DIA or .MZML file
70 -f background FASTA file
71 86
72 Other Parameters: 87 **Inputs**
73 -t target FASTA file (default: background FASTA file) 88
74 -tp true/false target FASTA file contains peptides (default: false) 89
75 -o output report file (default: [input file].pecan.txt) 90 - A spectrum file in mzML format
76 -acquisition (default: overlapping dia) 91 - A protein data base in fasta format
77 -addDecoysToBackground (default: false) 92
78 -alpha (default: 1.8) 93
79 -beta (default: 0.4) 94 @MSCONVERT_HELP@
80 -dontRunDecoys (default: false) 95
81 -enzyme (default: trypsin) 96 **Outputs**
82 -filterPeaklists (default: false) 97
83 -fixed (default: C=57.0214635) 98 - A log file
84 -foffset (default: 0) 99 - The identified features in tabular format
85 -frag (default: YONLY) 100 - The identified proteins in tabular format
86 -ftol (default: 10)
87 -ftolunits (default: ppm)
88 -maxCharge (default: 3)
89 -maxLength (default: 100)
90 -maxMissedCleavage (default: 1)
91 -minCharge (default: 2)
92 -minEluteTime (default: 12)
93 -minIntensity (default: -1.0)
94 -minLength (default: 5)
95 -minNumOfQuantitativePeaks (default: 3)
96 -minQuantitativeIonNumber (default: 3)
97 -numberOfQuantitativePeaks (default: 5)
98 -numberOfReportedPeaks (default: 1)
99 -numberOfThreadsUsed (default: 12)
100 -percolatorProteinThreshold (default: 0.01)
101 -percolatorThreshold (default: 0.01)
102 -percolatorVersionNumber (default: 3)
103 -poffset (default: 0)
104 -precursorIsolationMargin (default: 0)
105 -precursorWindowSize (default: -1)
106 -ptol (default: 10)
107 -ptolunits (default: ppm)
108 -requireVariableMods (default: false)
109 -variable (default: -)
110 101
111 ]]></help> 102 ]]></help>
112 <expand macro="citations" /> 103 <expand macro="citations" />
113 </tool> 104 </tool>