Mercurial > repos > jjohnson > encyclopedia_quantify

annotate encyclopedia_searchtolib.xml.bak @ 0:d3a6bc607825 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
author jjohnson
date Tue, 30 Jun 2020 11:34:57 -0400
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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_searchtolib" name="SearchToLib" version="@VERSION@.0">
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2 <description>Build a Chromatogram Library or quantify samples 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="exit_code"><![CDATA[
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8 @CMD_IMPORTS@
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9 @LINK_SCAN_INPUTS@
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10 @LINK_FASTA_INPUT@
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11 @LINK_TARGET_FASTA@
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12 @LINK_LIB_INPUT@
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13 for SCAN_FILE in `ls -1 inputs/*`; do
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14 echo "\$SCAN_FILE" &&
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15 EncyclopeDIA -Djava.awt.headless=true -Xmx20g
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16 #if not $l
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17 -walnut
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18 #end if
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19 -i \$SCAN_FILE
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20 @FASTA_INPUT@
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21 @TARGET_FASTA@
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22 @LIB_INPUT@
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23 @COMMON_OPTIONS@
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24 @MASS_LIBRARY_TOLERANCE@
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25 @PERCOLATOR_OPTIONS@
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26 @PEAK_OPTIONS@
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27 @WINDOW_OPTIONS@
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28 @MODIFICATION_OPTIONS@
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29 @SEARCH_OPTIONS@ | tee -a search2lib.log
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30 ; done &&
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31 EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
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32 #if not $l
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33 -pecan
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34 #end if
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35 @SCAN_INPUTS@
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36 @FASTA_INPUT@
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37 @TARGET_FASTA@
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38 @LIB_INPUT@
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39 -a $a
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40 -o chromatogram_library.elib
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41 | tee -a search2lib.log
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42 ]]></command>
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43 <inputs>
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44 <expand macro="scan_inputs"/>
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45 <expand macro="lib_input" optional="true" libhelp="Use a Chromatogram elib for quantification, or a Prosit dlib spectral library to make a chromatogram elib using EncyclopeDIA, or else leave blank to make a Chromatogram library from just the fasta using Walnut"/>
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46 <expand macro="fasta_input"/>
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47 <expand macro="target_fasta"/>
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48 <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files" help="retention-time alignment of peptides should be enabled when quantifying samples"/>
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49 <expand macro="common_options"/>
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50 <expand macro="mass_library_tolerance"/>
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51 <expand macro="percolator_options"/>
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52 <expand macro="peak_options"/>
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53 <expand macro="window_options"/>
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54 <expand macro="modification_options"/>
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55 <expand macro="search_options"/>
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56 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
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57 <option value="log" selected="true">log</option>
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58 <option value="elib" selected="true">elib</option>
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59 <option value="features" selected="true">concatenated_features.txt</option>
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60 <option value="results" selected="true">concatenated_results.txt</option>
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61 <option value="decoy" selected="false">concatenated_decoy.txt</option>
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62 <option value="peptides" selected="true">peptides.txt (requires match between runs)</option>
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63 <option value="proteins" selected="true">proteins.txt (requires match between runs)</option>
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64 </param>
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65 </inputs>
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66 <outputs>
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67 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
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68 <filter>'log' in select_outputs</filter>
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69 </data>
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70 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib">
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71 <filter>'elib' in select_outputs</filter>
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72 </data>
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73 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt">
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74 <filter>'features' in select_outputs</filter>
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75 <actions>
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76 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
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77 </actions>
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78 </data>
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79 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt">
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80 <filter>'results' in select_outputs</filter>
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81 <actions>
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82 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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83 </actions>
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84 </data>
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85 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt">
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86 <filter>'decoy' in select_outputs</filter>
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87 <actions>
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88 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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89 </actions>
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90 </data>
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91 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt">
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92 <filter>a and 'peptides' in select_outputs</filter>
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93 <actions>
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94 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
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95 </actions>
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96 </data>
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97 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt">
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98 <filter>a and 'proteins' in select_outputs</filter>
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99 <actions>
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100 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
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101 </actions>
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102 </data>
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103 </outputs>
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104 <help><![CDATA[
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105
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106 **SearchToLIB**
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107
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108 @ENCYCLOPEDIA_WIKI@
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109
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110 SearchToLIB uses the EncyclopeDIA algorithm, or the Walnut (Pecan) algorithm to search Data-Independent Acquisition (DIA) MS/MS spectrum files and creates a DIA elib chromatogram library for EncyclopeDIA DIA quantitation search.
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111
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112 SearchToLIB can also quantify peptides from the chromatogram library.
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113
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114 @MSCONVERT_HELP@
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115
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116 **Typical DIA SearchToLib Workflow**
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117
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118 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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119
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120 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library.
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121 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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122 Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring.
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123
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124
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125 * 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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126
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127
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128 2. SearchToLib 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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129
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130 .. image:: SearchToLib_Workflow.png
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131 :height: 439
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132 :width: 768
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133
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134 .. _Prosit: https://www.proteomicsdb.org/prosit
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135
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136 ]]></help>
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137 <expand macro="citations" />
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138 </tool>