Mercurial > repos > jjohnson > encyclopedia_quantify

annotate encyclopedia_quantify.xml @ 1:acf6acfc8632 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
author jjohnson
date Wed, 01 Jul 2020 11:24:39 -0400
parents d3a6bc607825
children aa52f0eadc85
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d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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1 <tool id="encyclopedia_quantify" name="EncyclopeDIA Quantify" version="@VERSION@.0">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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2 <description>samples from Data-Independent Acquisition (DIA) MS/MS Data</description>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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3 <macros>
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4 <import>macros.xml</import>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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5 </macros>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CMD_IMPORTS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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9 @LINK_SCAN_INPUTS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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10 @LINK_FASTA_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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11 @LINK_TARGET_FASTA@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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12 @LINK_LIB_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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13 for SCAN_FILE in `ls -1 inputs/*`; do
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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14 echo "\$SCAN_FILE" &&
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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15 EncyclopeDIA -Djava.awt.headless=true -Xmx20g
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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16 -i \$SCAN_FILE
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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17 @FASTA_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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18 @TARGET_FASTA@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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19 @LIB_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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20 @COMMON_OPTIONS@
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21 @MASS_LIBRARY_TOLERANCE@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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22 @PERCOLATOR_OPTIONS@
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23 @PEAK_OPTIONS@
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24 @WINDOW_OPTIONS@
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25 @MODIFICATION_OPTIONS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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26 @SEARCH_OPTIONS@ | tee -a search2lib.log
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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27 ; done &&
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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28 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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29 @SCAN_INPUTS@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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30 @FASTA_INPUT@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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31 @TARGET_FASTA@
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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32 @LIB_INPUT@
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33 -a $a
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34 -o chromatogram_library.elib
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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35 | tee -a search2lib.log
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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36 ]]></command>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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37 <inputs>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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38 <expand macro="scan_inputs"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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39 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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40 <expand macro="fasta_input"/>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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41 <expand macro="target_fasta"/>
1
acf6acfc8632 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
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42 <expand macro="options_section"/>
0
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43 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/>
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44 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
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45 <option value="log" selected="true">log</option>
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46 <option value="elib" selected="true">elib</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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47 <option value="features" selected="true">concatenated_features.txt</option>
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48 <option value="results" selected="true">concatenated_results.txt</option>
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49 <option value="decoy" selected="false">concatenated_decoy.txt</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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50 <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
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51 <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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52 </param>
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53 </inputs>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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54 <outputs>
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55 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
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56 <filter>'log' in select_outputs</filter>
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57 </data>
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58 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib">
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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59 <filter>'elib' in select_outputs</filter>
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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60 </data>
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61 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt">
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62 <filter>'features' in select_outputs</filter>
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63 <actions>
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64 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
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65 </actions>
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66 </data>
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67 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt">
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68 <filter>'results' in select_outputs</filter>
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69 <actions>
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70 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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71 </actions>
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72 </data>
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73 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt">
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74 <filter>'decoy' in select_outputs</filter>
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75 <actions>
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76 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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77 </actions>
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78 </data>
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79 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt">
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80 <filter>a and 'peptides' in select_outputs</filter>
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81 <actions>
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82 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
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83 </actions>
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84 </data>
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85 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt">
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86 <filter>a and 'proteins' in select_outputs</filter>
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87 <actions>
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88 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
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89 </actions>
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90 </data>
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91 </outputs>
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92 <help><![CDATA[
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93
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94 **EncyclopeDIA Quantify**
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95
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96 @ENCYCLOPEDIA_WIKI@
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97
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98 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results.
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99
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100 @MSCONVERT_HELP@
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101
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102 **Typical DIA SearchToLib Workflow**
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103
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104 Two sets of Mass Spec MS/MS DIA data are collected for the experiment. In addition to collecting wide-window DIA experiments on each quantitative replicate, a pool containing peptides from every condition is measured using several staggered narrow-window DIA experiments.
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105
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106 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library.
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107 If a Spectral library argument is provided, for example from **Prosit**, SearchToLIB uses EncyclopeDIA to search each input spectrum mzML file.
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108 Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring.
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109
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110
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111 * Prosit_ generates a predicted spectrum library of fragmentation patterns and retention times for every +2H and +3H tryptic peptide in a FASTA database, with up to one missed cleavage.
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112
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113
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114 2. EncyclopeDIA Quantify is then run on the wide-window quantitative replicate mzML files using that chromatogram library, with the *align between files* option, to produce quantification results.
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115
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116 .. image:: SearchToLib_Workflow.png
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117 :width: 810
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118 :height: 580
0
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119
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120 .. _Prosit: https://www.proteomicsdb.org/prosit
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121
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122 ]]></help>
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123 <expand macro="citations" />
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124 </tool>