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comparison encyclopedia_encyclopedia.xml @ 1:f3a4d2a41393 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"
author galaxyp
date Mon, 14 Sep 2020 16:57:41 +0000
parents 3070c42052ab
children 745cf6f2e8ac
comparison
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0:3070c42052ab 1:f3a4d2a41393
2 <description>Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data</description> 2 <description>Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 @CMD_IMPORTS@ 8 @CMD_IMPORTS@
9 @LINK_SCAN_INPUT@ 9 @LINK_SCAN_INPUT@
10 @LINK_FASTA_INPUT@ 10 @LINK_FASTA_INPUT@
11 @LINK_LIB_INPUT@ 11 @LINK_LIB_INPUT@
12 EncyclopeDIA -Djava.awt.headless=true 12 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
13 -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
14 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
13 @SCAN_INPUT@ 15 @SCAN_INPUT@
14 @FASTA_INPUT@ 16 @FASTA_INPUT@
15 @LIB_INPUT@ 17 @LIB_INPUT@
16 @COMMON_OPTIONS@ 18 @COMMON_OPTIONS@
17 @MASS_LIBRARY_TOLERANCE@ 19 @MASS_LIBRARY_TOLERANCE@
22 -o gxpedia 24 -o gxpedia
23 ]]></command> 25 ]]></command>
24 <inputs> 26 <inputs>
25 <expand macro="scan_input"/> 27 <expand macro="scan_input"/>
26 <expand macro="fasta_input"/> 28 <expand macro="fasta_input"/>
27 <expand macro="lib_input" token_optional="false" token_help="Chromatogram elib from SearchToLib"/> 29 <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
28 <expand macro="common_options"/> 30 <expand macro="options_section"/>
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"> 31 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
35 <option value="log" selected="true">log</option> 32 <option value="log" selected="true">log</option>
36 <option value="elib" selected="true">elib</option> 33 <option value="elib" selected="true">elib</option>
37 <option value="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option> 34 <option value="first_delta_rt_pdf" selected="false">Initial Delta Retention Time Plot</option>
38 <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option> 35 <option value="first_rt_fit_pdf" selected="false">Initial Fitted Retention Time Plot</option>
39 <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option> 36 <option value="first_rt_fit_txt" selected="false">Initial Fitted Retention Time Table</option>
40 <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option> 37 <option value="final_delta_rt_pdf" selected="false">Final Delta Retention Time Plot</option>
41 <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option> 38 <option value="final_rt_fit_pdf" selected="false">Final Fitted Retention Time Plot</option>
42 <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option> 39 <option value="final_rt_fit_txt" selected="false">Final Fitted Retention Time Table</option>
43 <option value="features" selected="true">features.txt</option> 40 <option value="features" selected="false">features</option>
44 <option value="encyclopedia" selected="true">encyclopedia.txt</option> 41 <option value="encyclopedia" selected="true">encyclopedia results</option>
45 <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option> 42 <option value="encyclopedia_decoy" selected="false">encyclopedia decoy results</option>
46 </param> 43 </param>
47 </inputs> 44 </inputs>
48 <outputs> 45 <outputs>
49 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> 46 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
50 <filter>'log' in select_outputs</filter> 47 <filter>'log' in select_outputs</filter>
93 <actions> 90 <actions>
94 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> 91 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
95 </actions> 92 </actions>
96 </data> 93 </data>
97 </outputs> 94 </outputs>
95 <tests>
96 <test>
97 <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
98 <param name="library" ftype="elib" value="BCS_hela.elib"/>
99 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
100 <param name="select_outputs" value="log,features,encyclopedia"/>
101 <output name="features" ftype="tabular">
102 <assert_contents>
103 <has_text text="ESYDDVSSFR"/>
104 </assert_contents>
105 </output>
106 <output name="encyclopedia" ftype="tabular">
107 <assert_contents>
108 <has_text text="ESYDDVSSFR"/>
109 </assert_contents>
110 </output>
111 </test>
112 </tests>
113
98 <help><![CDATA[ 114 <help><![CDATA[
99 EncyclopeDIA is a library search engine for DIA data. 115 **EncyclopeDIA**
100 You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb
101 116
102 Required Parameters: 117 @ENCYCLOPEDIA_WIKI@
103 -i input .DIA or .MZML file
104 -f protein .FASTA database
105 -l library .ELIB file
106 118
107 Other Parameters: 119 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) 120
109 -acquisition (default: Non-Overlapping DIA) 121
110 -enzyme (default: trypsin) 122 **Inputs**
111 -expectedPeakWidth (default: 25) 123
112 -filterPeaklists (default: false) 124 - A spectrum file in mzML format
113 -fixed (default: C=57.0214635) 125 - A chromatogram library that can be generated by SearchToLib
114 -foffset (default: 0) 126 - A protein data base in fasta format
115 -frag (default: CID) 127
116 -ftol (default: 10) 128
117 -ftolunits (default: ppm) 129 @MSCONVERT_HELP@
118 -lftol (default: 10) 130
119 -lftolunits (default: ppm) 131 **Outputs**
120 -localizationModification (default: none) 132
121 -minIntensity (default: -1.0) 133 - A log file
122 -minNumOfQuantitativePeaks (default: 3) 134 - A Chromatogram Library (.elib)
123 -minQuantitativeIonNumber (default: 3) 135 - The identified features in tabular format
124 -numberOfExtraDecoyLibrariesSearched (default: 0.0) 136 Feature values of scans that are used by percolator to determine matches.
125 -numberOfQuantitativePeaks (default: 5) 137 - The identified Peptide Spectral Match results in tabular format
126 -percolatorProteinThreshold (default: 0.01) 138 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
127 -percolatorThreshold (default: 0.01) 139 - The identified peptides in tabular format
128 -percolatorVersionNumber (default: 3) 140 Per peptide: the normalized intensity for each scan file.
129 -poffset (default: 0) 141 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
130 -precursorIsolationMargin (default: 0) 142 - The identified proteins in tabular format
131 -precursorWindowSize (default: -1) 143 Per protein: the normalized intensity for each scan file.
132 -ptol (default: 10) 144 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
133 -ptolunits (default: ppm)
134 -rtWindowInMin (default: -1.0)
135 -scoringBreadthType (default: window)
136 -verifyModificationIons (default: true)
137 145
138 ]]></help> 146 ]]></help>
139 <expand macro="citations" /> 147 <expand macro="citations" />
140 </tool> 148 </tool>