Mercurial > repos > jjohnson > encyclopedia_encyclopedia

comparison encyclopedia_encyclopedia.xml @ 0:36f9910c85c4 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 10:13:10 -0400
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children b4f1a49ff3b5
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-1:000000000000 0:36f9910c85c4
1 <tool id="encyclopedia_encyclopedia" name="EncyclopeDIA" version="@VERSION@.0">
2 <description>Library Searching 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_LIB_INPUT@
12 EncyclopeDIA -Djava.awt.headless=true
13 @SCAN_INPUT@
14 @FASTA_INPUT@
15 @LIB_INPUT@
16 @COMMON_OPTIONS@
17 @MASS_LIBRARY_TOLERANCE@
18 @PERCOLATOR_OPTIONS@
19 @PEAK_OPTIONS@
20 @WINDOW_OPTIONS@
21 @MODIFICATION_OPTIONS@
22 -o gxpedia
23 ]]></command>
24 <inputs>
25 <expand macro="scan_input"/>
26 <expand macro="fasta_input"/>
27 <expand macro="lib_input" token_optional="false" token_help="Chromatogram elib from SearchToLib"/>
28 <expand macro="common_options"/>
29 <expand macro="mass_library_tolerance"/>
30 <expand macro="percolator_options"/>
31 <expand macro="peak_options"/>
32 <expand macro="window_options"/>
33 <expand macro="modification_options"/>
34 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
35 <option value="log" selected="true">log</option>
36 <option value="elib" selected="true">elib</option>
37 <option value="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option>
38 <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option>
39 <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option>
40 <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option>
41 <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option>
42 <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option>
43 <option value="features" selected="true">features.txt</option>
44 <option value="encyclopedia" selected="true">encyclopedia.txt</option>
45 <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option>
46 </param>
47 </inputs>
48 <outputs>
49 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
50 <filter>'log' in select_outputs</filter>
51 </data>
52 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
53 <filter>'elib' in select_outputs</filter>
54 </data>
55 <data name="first_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.delta_rt.pdf">
56 <filter>'first_delta_rt_pdf' in select_outputs</filter>
57 </data>
58 <data name="first_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.pdf">
59 <filter>'first_rt_fit_pdf' in select_outputs</filter>
60 </data>
61 <data name="first_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.txt">
62 <filter>'first_rt_fit_txt' in select_outputs</filter>
63 <actions>
64 <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" />
65 </actions>
66 </data>
67 <data name="final_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.delta_rt.pdf">
68 <filter>'final_delta_rt_pdf' in select_outputs</filter>
69 </data>
70 <data name="final_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.pdf">
71 <filter>'final_rt_fit_pdf' in select_outputs</filter>
72 </data>
73 <data name="final_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.txt">
74 <filter>'final_rt_fit_txt' in select_outputs</filter>
75 <actions>
76 <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" />
77 </actions>
78 </data>
79 <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
80 <filter>'features' in select_outputs</filter>
81 <actions>
82 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,deltaCN,primary,xCorrLib,xCorrModel,LogDotProduct,logWeightedDotProduct,sumOfSquaredErrors,weightedSumOfSquaredErrors,numberOfMatchingPeaks,numberOfMatchingPeaksAboveThreshold,averageAbsFragmentDeltaMass,averageFragmentDeltaMasses,isotopeDotProduct,averageAbsParentDeltaMass,averageParentDeltaMass,eValue,deltaRT,pepLength,charge2,charge3,precursorMz,RTinMin,sequence,protein" />
83 </actions>
84 </data>
85 <data name="encyclopedia" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt" from_work_dir="gxpedia.encyclopedia.txt">
86 <filter>'encyclopedia' in select_outputs</filter>
87 <actions>
88 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
89 </actions>
90 </data>
91 <data name="encyclopedia_decoy" format="tabular" label="${tool.name} ${on_string} encyclopedia.decoy.txt" from_work_dir="gxpedia.encyclopedia.decoy.txt">
92 <filter>'encyclopedia_decoy' in select_outputs</filter>
93 <actions>
94 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
95 </actions>
96 </data>
97 </outputs>
98 <help><![CDATA[
99 EncyclopeDIA is a library search engine for DIA data.
100 You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
101
102 Required Parameters:
103 -i input .DIA or .MZML file
104 -f protein .FASTA database
105 -l library .ELIB file
106
107 Other Parameters:
108 -o output report file (default: [input file].encyclopedia.txt)
109 -acquisition (default: Non-Overlapping DIA)
110 -enzyme (default: trypsin)
111 -expectedPeakWidth (default: 25)
112 -filterPeaklists (default: false)
113 -fixed (default: C=57.0214635)
114 -foffset (default: 0)
115 -frag (default: CID)
116 -ftol (default: 10)
117 -ftolunits (default: ppm)
118 -lftol (default: 10)
119 -lftolunits (default: ppm)
120 -localizationModification (default: none)
121 -minIntensity (default: -1.0)
122 -minNumOfQuantitativePeaks (default: 3)
123 -minQuantitativeIonNumber (default: 3)
124 -numberOfExtraDecoyLibrariesSearched (default: 0.0)
125 -numberOfQuantitativePeaks (default: 5)
126 -percolatorProteinThreshold (default: 0.01)
127 -percolatorThreshold (default: 0.01)
128 -percolatorVersionNumber (default: 3)
129 -poffset (default: 0)
130 -precursorIsolationMargin (default: 0)
131 -precursorWindowSize (default: -1)
132 -ptol (default: 10)
133 -ptolunits (default: ppm)
134 -rtWindowInMin (default: -1.0)
135 -scoringBreadthType (default: window)
136 -verifyModificationIons (default: true)
137
138 ]]></help>
139 <expand macro="citations" />
140 </tool>