Mercurial > repos > jjohnson > encyclopedia_walnut

annotate encyclopedia_walnut.xml @ 7:7556b19daa48 draft

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"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
children
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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" />
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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>
5
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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.
925fffecea81 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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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
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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
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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
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100 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
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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, ...
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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>