Mercurial > repos > jjohnson > encyclopedia_encyclopedia

comparison encyclopedia_encyclopedia.xml @ 1:b4f1a49ff3b5 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"
author jjohnson
date Tue, 30 Jun 2020 11:39:02 -0400
parents 36f9910c85c4
children 79d2deca24b8
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0:36f9910c85c4 1:b4f1a49ff3b5
22 -o gxpedia 22 -o gxpedia
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <expand macro="scan_input"/> 25 <expand macro="scan_input"/>
26 <expand macro="fasta_input"/> 26 <expand macro="fasta_input"/>
27 <expand macro="lib_input" token_optional="false" token_help="Chromatogram elib from SearchToLib"/> 27 <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
28 <expand macro="common_options"/> 28 <expand macro="common_options"/>
29 <expand macro="mass_library_tolerance"/> 29 <expand macro="mass_library_tolerance"/>
30 <expand macro="percolator_options"/> 30 <expand macro="percolator_options"/>
31 <expand macro="peak_options"/> 31 <expand macro="peak_options"/>
32 <expand macro="window_options"/> 32 <expand macro="window_options"/>
94 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 94 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
95 </actions> 95 </actions>
96 </data> 96 </data>
97 </outputs> 97 </outputs>
98 <help><![CDATA[ 98 <help><![CDATA[
99 EncyclopeDIA is a library search engine for DIA data. 99 **EncyclopeDIA**
100 You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
101 100
102 Required Parameters: 101 @ENCYCLOPEDIA_WIKI@
103 -i input .DIA or .MZML file
104 -f protein .FASTA database
105 -l library .ELIB file
106 102
107 Other Parameters: 103 EncyclopeDIA extracts peptide fragmentation chromatograms from MZML files, matches them to spectra in libraries, and calculates various scoring features. These features are interpreted by Percolator to identify peptides.
108 -o output report file (default: [input file].encyclopedia.txt) 104
109 -acquisition (default: Non-Overlapping DIA) 105
110 -enzyme (default: trypsin) 106 **Inputs**
111 -expectedPeakWidth (default: 25) 107
112 -filterPeaklists (default: false) 108
113 -fixed (default: C=57.0214635) 109 - A spectrum file in mzML format
114 -foffset (default: 0) 110 - A chromatogram library that can be generated by SearchToLib
115 -frag (default: CID) 111 - A protein data base in fasta format
116 -ftol (default: 10) 112
117 -ftolunits (default: ppm) 113
118 -lftol (default: 10) 114 @MSCONVERT_HELP@
119 -lftolunits (default: ppm) 115
120 -localizationModification (default: none) 116 **Outputs**
121 -minIntensity (default: -1.0) 117
122 -minNumOfQuantitativePeaks (default: 3) 118 - A log file
123 -minQuantitativeIonNumber (default: 3) 119 - The identified features in tabular format
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)
137 120
138 ]]></help> 121 ]]></help>
139 <expand macro="citations" /> 122 <expand macro="citations" />
140 </tool> 123 </tool>