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comparison encyclopedia_walnut.xml @ 0:ce1a157a41bd 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 17:06:23 +0000
parents
children d6a4dfdad269
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-1:000000000000 0:ce1a157a41bd
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="aggressive"><![CDATA[
8 @CMD_IMPORTS@
9 @LINK_SCAN_INPUT@
10 @LINK_FASTA_INPUT@
11 @LINK_TARGET_FASTA@
12 EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
13 -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -walnut
14 -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
15 @SCAN_INPUT@
16 @FASTA_INPUT@
17 @TARGET_FASTA@
18 @COMMON_OPTIONS@
19 @MASS_LIBRARY_TOLERANCE@
20 @PERCOLATOR_OPTIONS@
21 @PEAK_OPTIONS@
22 @WINDOW_OPTIONS@
23 @MODIFICATION_OPTIONS@
24 @SEARCH_OPTIONS@
25 -o gxpedia
26 ]]></command>
27 <inputs>
28 <expand macro="scan_input"/>
29 <expand macro="fasta_input"/>
30 <expand macro="target_fasta"/>
31 <expand macro="options_section"/>
32 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
33 <option value="log" selected="true">log</option>
34 <option value="elib" selected="true">elib</option>
35 <option value="features" selected="false">features.txt</option>
36 <option value="pecan" selected="true">pecan.txt</option>
37 <option value="pecan_decoy" selected="false">pecan.decoy.txt</option>
38 </param>
39 </inputs>
40 <outputs>
41 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
42 <filter>'log' in select_outputs</filter>
43 </data>
44 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
45 <filter>'elib' in select_outputs</filter>
46 </data>
47 <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
48 <filter>'features' in select_outputs</filter>
49 <actions>
50 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
51 </actions>
52 </data>
53 <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt">
54 <filter>'pecan' in select_outputs</filter>
55 <actions>
56 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
57 </actions>
58 </data>
59 <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt">
60 <filter>'pecan_decoy' in select_outputs</filter>
61 <actions>
62 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
63 </actions>
64 </data>
65 </outputs>
66 <tests>
67 <test>
68 <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/>
69 <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/>
70 <param name="select_outputs" value="log,features,pecan"/>
71 <output name="features" ftype="tabular">
72 <assert_contents>
73 <has_text text="LHYNEGLNIK"/>
74 </assert_contents>
75 </output>
76 </test>
77 </tests>
78 <help><![CDATA[
79 **Walnut**
80
81 @ENCYCLOPEDIA_WIKI@
82
83 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
84 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.
85
86
87
88 **Inputs**
89
90 - A spectrum file in mzML format
91 - A protein data base in fasta format
92
93 @MSCONVERT_HELP@
94
95 **Outputs**
96
97 - A log file
98 - A Chromatogram Library (.elib)
99 - The identified features in tabular format
100 Feature values of scans that are used by percolator to determine matches.
101 - The identified Peptide Spectral Match results in tabular format
102 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
103 - The identified peptides in tabular format
104 Per peptide: the normalized intensity for each scan file.
105 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
106 - The identified proteins in tabular format
107 Per protein: the normalized intensity for each scan file.
108 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
109
110
111 ]]></help>
112 <expand macro="citations" />
113 </tool>