annotate encyclopedia_walnut.xml @ 7:7556b19daa48 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit dd611a143e4e003a5fb085cdf93ae477cc5ea0b1"
author jjohnson
date Wed, 26 Aug 2020 14:42:51 -0400
parents 0172dfa08216
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1 <tool id="encyclopedia_walnut" name="Walnut" version="@VERSION@.0">
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2 <description>PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
4
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7 <command detect_errors="aggressive"><![CDATA[
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8 @CMD_IMPORTS@
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9 @LINK_SCAN_INPUT@
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10 @LINK_FASTA_INPUT@
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11 @LINK_TARGET_FASTA@
7
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12 EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -walnut
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13 @SCAN_INPUT@
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14 @FASTA_INPUT@
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15 @TARGET_FASTA@
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16 @COMMON_OPTIONS@
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17 @MASS_LIBRARY_TOLERANCE@
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18 @PERCOLATOR_OPTIONS@
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19 @PEAK_OPTIONS@
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20 @WINDOW_OPTIONS@
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21 @MODIFICATION_OPTIONS@
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22 @SEARCH_OPTIONS@
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23 -o gxpedia
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24 ]]></command>
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25 <inputs>
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26 <expand macro="scan_input"/>
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27 <expand macro="fasta_input"/>
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28 <expand macro="target_fasta"/>
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29 <expand macro="options_section"/>
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30 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
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31 <option value="log" selected="true">log</option>
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32 <option value="elib" selected="true">elib</option>
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33 <option value="features" selected="false">features.txt</option>
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34 <option value="pecan" selected="true">pecan.txt</option>
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35 <option value="pecan_decoy" selected="false">pecan.decoy.txt</option>
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36 </param>
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37 </inputs>
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38 <outputs>
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39 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
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40 <filter>'log' in select_outputs</filter>
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41 </data>
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42 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
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43 <filter>'elib' in select_outputs</filter>
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44 </data>
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45 <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
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46 <filter>'features' in select_outputs</filter>
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47 <actions>
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48 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
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49 </actions>
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50 </data>
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51 <data name="pecan" format="tabular" label="${tool.name} ${on_string} pecan.txt" from_work_dir="gxpedia.pecan.txt">
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52 <filter>'pecan' in select_outputs</filter>
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53 <actions>
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54 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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55 </actions>
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56 </data>
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57 <data name="pecan_decoy" format="tabular" label="${tool.name} ${on_string} pecan.decoy.txt" from_work_dir="gxpedia.pecan.decoy.txt">
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58 <filter>'pecan_decoy' in select_outputs</filter>
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59 <actions>
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60 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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61 </actions>
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62 </data>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/>
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67 <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/>
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68 <param name="select_outputs" value="log,features,pecan"/>
5
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69 <output name="features" ftype="tabular">
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70 <assert_contents>
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71 <has_text text="LHYNEGLNIK"/>
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72 </assert_contents>
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73 </output>
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74 </test>
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75 </tests>
0
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76 <help><![CDATA[
5
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77 **Walnut**
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78
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79 @ENCYCLOPEDIA_WIKI@
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80
0
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81 Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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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.
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83
5
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84
6
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85
5
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86 **Inputs**
4936de9f9024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
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87
4936de9f9024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
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88 - A spectrum file in mzML format
4936de9f9024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
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89 - A protein data base in fasta format
4936de9f9024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
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90
4936de9f9024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
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91 @MSCONVERT_HELP@
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92
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93 **Outputs**
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94
4936de9f9024 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
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95 - A log file
6
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96 - A Chromatogram Library (.elib)
0172dfa08216 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
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97 - The identified features in tabular format
0172dfa08216 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
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98 Feature values of scans that are used by percolator to determine matches.
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99 - The identified Peptide Spectral Match results in tabular format
0172dfa08216 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
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100 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
0172dfa08216 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
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101 - The identified peptides in tabular format
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102 Per peptide: the normalized intensity for each scan file.
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103 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
0172dfa08216 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
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104 - The identified proteins in tabular format
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105 Per protein: the normalized intensity for each scan file.
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106 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
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107
0
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108
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109 ]]></help>
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110 <expand macro="citations" />
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111 </tool>