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comparison encyclopedia_walnut.xml @ 0:9002bb1c248d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author galaxyp
date Fri, 19 Jun 2020 14:04:16 +0000
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children d44902652df2
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-1:000000000000 0:9002bb1c248d
1 <tool id="encyclopedia_walnut" name="Walnut" version="@VERSION@.0">
2 <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 @CMD_IMPORTS@
9 @LINK_SCAN_INPUT@
10 @LINK_FASTA_INPUT@
11 @LINK_TARGET_FASTA@
12 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -walnut
13 @SCAN_INPUT@
14 @FASTA_INPUT@
15 @TARGET_FASTA@
16 @COMMON_OPTIONS@
17 @MASS_LIBRARY_TOLERANCE@
18 @PERCOLATOR_OPTIONS@
19 @PEAK_OPTIONS@
20 @WINDOW_OPTIONS@
21 @MODIFICATION_OPTIONS@
22 @SEARCH_OPTIONS@
23 -o gxpedia
24 ]]></command>
25 <inputs>
26 <expand macro="scan_input"/>
27 <expand macro="fasta_input"/>
28 <expand macro="target_fasta"/>
29 <expand macro="common_options"/>
30 <expand macro="mass_library_tolerance"/>
31 <expand macro="percolator_options"/>
32 <expand macro="peak_options"/>
33 <expand macro="window_options"/>
34 <expand macro="modification_options"/>
35 <expand macro="search_options"/>
36 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
37 <option value="log" selected="true">log</option>
38 <option value="elib" selected="true">elib</option>
39 <option value="features" selected="true">features.txt</option>
40 <option value="pecan" selected="true">pecan.txt</option>
41 <option value="pecan_decoy" selected="true">pecan.decoy.txt</option>
42 </param>
43 </inputs>
44 <outputs>
45 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
46 <filter>'log' in select_outputs</filter>
47 </data>
48 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
49 <filter>'elib' in select_outputs</filter>
50 </data>
51 <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
52 <filter>'features' in select_outputs</filter>
53 <actions>
54 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
55 </actions>
56 </data>
57 <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt">
58 <filter>'pecan' in select_outputs</filter>
59 <actions>
60 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
61 </actions>
62 </data>
63 <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt">
64 <filter>'pecan_decoy' in select_outputs</filter>
65 <actions>
66 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
67 </actions>
68 </data>
69 </outputs>
70 <help><![CDATA[
71 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
72 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.
73
74 Required Parameters:
75 -i input .DIA or .MZML file
76 -f background FASTA file
77
78 Other Parameters:
79 -t target FASTA file (default: background FASTA file)
80 -tp true/false target FASTA file contains peptides (default: false)
81 -o output report file (default: [input file].pecan.txt)
82 -acquisition (default: overlapping dia)
83 -addDecoysToBackground (default: false)
84 -alpha (default: 1.8)
85 -beta (default: 0.4)
86 -dontRunDecoys (default: false)
87 -enzyme (default: trypsin)
88 -filterPeaklists (default: false)
89 -fixed (default: C=57.0214635)
90 -foffset (default: 0)
91 -frag (default: YONLY)
92 -ftol (default: 10)
93 -ftolunits (default: ppm)
94 -maxCharge (default: 3)
95 -maxLength (default: 100)
96 -maxMissedCleavage (default: 1)
97 -minCharge (default: 2)
98 -minEluteTime (default: 12)
99 -minIntensity (default: -1.0)
100 -minLength (default: 5)
101 -minNumOfQuantitativePeaks (default: 3)
102 -minQuantitativeIonNumber (default: 3)
103 -numberOfQuantitativePeaks (default: 5)
104 -numberOfReportedPeaks (default: 1)
105 -numberOfThreadsUsed (default: 12)
106 -percolatorProteinThreshold (default: 0.01)
107 -percolatorThreshold (default: 0.01)
108 -percolatorVersionNumber (default: 3)
109 -poffset (default: 0)
110 -precursorIsolationMargin (default: 0)
111 -precursorWindowSize (default: -1)
112 -ptol (default: 10)
113 -ptolunits (default: ppm)
114 -requireVariableMods (default: false)
115 -variable (default: -)
116
117 ]]></help>
118 <expand macro="citations" />
119 </tool>