Mercurial > repos > jjohnson > encyclopedia_walnut
comparison encyclopedia_walnut.xml @ 6:0172dfa08216 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
author | jjohnson |
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date | Fri, 21 Aug 2020 16:13:00 -0400 |
parents | 4936de9f9024 |
children | 7556b19daa48 |
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5:4936de9f9024 | 6:0172dfa08216 |
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28 <expand macro="target_fasta"/> | 28 <expand macro="target_fasta"/> |
29 <expand macro="options_section"/> | 29 <expand macro="options_section"/> |
30 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> | 30 <param name="select_outputs" type="select" label="Select outputs" multiple="true"> |
31 <option value="log" selected="true">log</option> | 31 <option value="log" selected="true">log</option> |
32 <option value="elib" selected="true">elib</option> | 32 <option value="elib" selected="true">elib</option> |
33 <option value="features" selected="true">features.txt</option> | 33 <option value="features" selected="false">features.txt</option> |
34 <option value="pecan" selected="true">pecan.txt</option> | 34 <option value="pecan" selected="true">pecan.txt</option> |
35 <option value="pecan_decoy" selected="true">pecan.decoy.txt</option> | 35 <option value="pecan_decoy" selected="false">pecan.decoy.txt</option> |
36 </param> | 36 </param> |
37 </inputs> | 37 </inputs> |
38 <outputs> | 38 <outputs> |
39 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> | 39 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log"> |
40 <filter>'log' in select_outputs</filter> | 40 <filter>'log' in select_outputs</filter> |
63 </outputs> | 63 </outputs> |
64 <tests> | 64 <tests> |
65 <test> | 65 <test> |
66 <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/> | 66 <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/> |
67 <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/> | 67 <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/> |
68 <param name="select_outputs" values="log,features,pecan"/> | |
68 <output name="features" ftype="tabular"> | 69 <output name="features" ftype="tabular"> |
69 <assert_contents> | 70 <assert_contents> |
70 <has_text text="LHYNEGLNIK"/> | 71 <has_text text="LHYNEGLNIK"/> |
71 </assert_contents> | 72 </assert_contents> |
72 </output> | 73 </output> |
73 </test> | 74 </test> |
74 </tests> | 75 </tests> |
75 <help><![CDATA[ | 76 <help><![CDATA[ |
76 | |
77 <help><![CDATA[ | |
78 | |
79 **Walnut** | 77 **Walnut** |
80 | 78 |
81 @ENCYCLOPEDIA_WIKI@ | 79 @ENCYCLOPEDIA_WIKI@ |
82 | 80 |
83 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data. | 81 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. | 82 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 | 83 |
86 | 84 |
85 | |
87 **Inputs** | 86 **Inputs** |
88 | |
89 | 87 |
90 - A spectrum file in mzML format | 88 - A spectrum file in mzML format |
91 - A protein data base in fasta format | 89 - A protein data base in fasta format |
92 | |
93 | 90 |
94 @MSCONVERT_HELP@ | 91 @MSCONVERT_HELP@ |
95 | 92 |
96 **Outputs** | 93 **Outputs** |
97 | 94 |
98 - A log file | 95 - A log file |
99 - The identified features in tabular format | 96 - A Chromatogram Library (.elib) |
100 - The identified proteins in tabular format | 97 - The identified features in tabular format |
98 Feature values of scans that are used by percolator to determine matches. | |
99 - The identified Peptide Spectral Match results in tabular format | |
100 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds | |
101 - The identified peptides in tabular format | |
102 Per peptide: the normalized intensity for each scan file. | |
103 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ... | |
104 - The identified proteins in tabular format | |
105 Per protein: the normalized intensity for each scan file. | |
106 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ... | |
107 | |
101 | 108 |
102 ]]></help> | 109 ]]></help> |
103 <expand macro="citations" /> | 110 <expand macro="citations" /> |
104 </tool> | 111 </tool> |