Mercurial > repos > jjohnson > encyclopedia_searchtolib

comparison encyclopedia_searchtolib.xml @ 0:683b98838cf0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author jjohnson
date Fri, 19 Jun 2020 10:21:31 -0400
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-1:000000000000 0:683b98838cf0
1 <tool id="encyclopedia_searchtolib" name="SearchToLib" 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_INPUTS@
10 @LINK_FASTA_INPUT@
11 @LINK_TARGET_FASTA@
12 @LINK_LIB_INPUT@
13 for SCAN_FILE in `ls -1 inputs/*`; do
14 echo "\$SCAN_FILE" &&
15 EncyclopeDIA -Djava.awt.headless=true -Xmx20g
16 #if not $l
17 -walnut
18 #end if
19 -i \$SCAN_FILE
20 @FASTA_INPUT@
21 @TARGET_FASTA@
22 @LIB_INPUT@
23 @COMMON_OPTIONS@
24 @MASS_LIBRARY_TOLERANCE@
25 @PERCOLATOR_OPTIONS@
26 @PEAK_OPTIONS@
27 @WINDOW_OPTIONS@
28 @MODIFICATION_OPTIONS@
29 @SEARCH_OPTIONS@ | tee -a search2lib.log
30 ; done &&
31 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
32 #if not $l
33 -pecan
34 #end if
35 @SCAN_INPUTS@
36 @FASTA_INPUT@
37 @TARGET_FASTA@
38 @LIB_INPUT@
39 ## @COMMON_OPTIONS@
40 ## @MASS_LIBRARY_TOLERANCE@
41 ## @PERCOLATOR_OPTIONS@
42 ## @PEAK_OPTIONS@
43 ## @WINDOW_OPTIONS@
44 ## @MODIFICATION_OPTIONS@
45 ## @SEARCH_OPTIONS@
46 -a $a
47 -o chromatogram_library.elib
48 | tee -a search2lib.log
49 ]]></command>
50 <inputs>
51 <expand macro="scan_inputs"/>
52 <expand macro="lib_input" token_optional="true" token_help="If a prosit dlib is supplied, use EncycopeDIA, else use walnut"/>
53 <expand macro="fasta_input"/>
54 <expand macro="target_fasta"/>
55 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="match between runs"/>
56 <expand macro="common_options"/>
57 <expand macro="mass_library_tolerance"/>
58 <expand macro="percolator_options"/>
59 <expand macro="peak_options"/>
60 <expand macro="window_options"/>
61 <expand macro="modification_options"/>
62 <expand macro="search_options"/>
63 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
64 <option value="log" selected="true">log</option>
65 <option value="elib" selected="true">elib</option>
66 <option value="features" selected="true">concatenated_features.txt</option>
67 <option value="results" selected="true">concatenated_results.txt</option>
68 <option value="decoy" selected="false">concatenated_decoy.txt</option>
69 <option value="peptides" selected="true">peptides.txt (requires match between runs)</option>
70 <option value="proteins" selected="true">proteins.txt (requires match between runs)</option>
71 </param>
72 </inputs>
73 <outputs>
74 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
75 <filter>'log' in select_outputs</filter>
76 </data>
77 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib">
78 <filter>'elib' in select_outputs</filter>
79 </data>
80 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt">
81 <filter>'features' in select_outputs</filter>
82 <actions>
83 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
84 </actions>
85 </data>
86 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt">
87 <filter>'results' in select_outputs</filter>
88 <actions>
89 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
90 </actions>
91 </data>
92 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt">
93 <filter>'decoy' in select_outputs</filter>
94 <actions>
95 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
96 </actions>
97 </data>
98 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt">
99 <filter>a and peptides' in select_outputs</filter>
100 <actions>
101 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
102 </actions>
103 </data>
104 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt">
105 <filter>a and 'proteins' in select_outputs</filter>
106 <actions>
107 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
108 </actions>
109 </data>
110 <!--
111 -->
112 </outputs>
113 <help><![CDATA[
114 SearchToLIB uses EncyclopeDIA, Walnut (Pecan), or XCorDIA to create an DIA Elib for EncyclopeDIA DIA search
115 Walnut is a FASTA database search engine for DIA data that uses PECAN-style scoring.
116 You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
117
118 Required Parameters:
119 -i input .DIA or .MZML file
120 -f background FASTA file
121
122 Other Parameters:
123 -t target FASTA file (default: background FASTA file)
124 -tp true/false target FASTA file contains peptides (default: false)
125 -o output report file (default: [input file].pecan.txt)
126 -acquisition (default: overlapping dia)
127 -addDecoysToBackground (default: false)
128 -alpha (default: 1.8)
129 -beta (default: 0.4)
130 -dontRunDecoys (default: false)
131 -enzyme (default: trypsin)
132 -filterPeaklists (default: false)
133 -fixed (default: C=57.0214635)
134 -foffset (default: 0)
135 -frag (default: YONLY)
136 -ftol (default: 10)
137 -ftolunits (default: ppm)
138 -maxCharge (default: 3)
139 -maxLength (default: 100)
140 -maxMissedCleavage (default: 1)
141 -minCharge (default: 2)
142 -minEluteTime (default: 12)
143 -minIntensity (default: -1.0)
144 -minLength (default: 5)
145 -minNumOfQuantitativePeaks (default: 3)
146 -minQuantitativeIonNumber (default: 3)
147 -numberOfQuantitativePeaks (default: 5)
148 -numberOfReportedPeaks (default: 1)
149 -numberOfThreadsUsed (default: 12)
150 -percolatorProteinThreshold (default: 0.01)
151 -percolatorThreshold (default: 0.01)
152 -percolatorVersionNumber (default: 3)
153 -poffset (default: 0)
154 -precursorIsolationMargin (default: 0)
155 -precursorWindowSize (default: -1)
156 -ptol (default: 10)
157 -ptolunits (default: ppm)
158 -requireVariableMods (default: false)
159 -variable (default: -)
160
161 ]]></help>
162 <expand macro="citations" />
163 </tool>