Mercurial > repos > jjohnson > encyclopedia_quantify

annotate encyclopedia_quantify.xml @ 6:5a5da160f667 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 14:39:14 -0400
parents 30f6b9c88ceb
children
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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>
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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_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@
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" &&
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15 EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
0
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16 -i \$SCAN_FILE
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17 @FASTA_INPUT@
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18 @TARGET_FASTA@
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19 @LIB_INPUT@
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20 @COMMON_OPTIONS@
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21 @MASS_LIBRARY_TOLERANCE@
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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@
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26 @SEARCH_OPTIONS@ | tee -a search2lib.log
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27 ; done &&
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28 for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
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29 EncyclopeDIA -Djava.awt.headless=true -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport
0
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30 @SCAN_INPUTS@
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31 @FASTA_INPUT@
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32 @TARGET_FASTA@
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33 @LIB_INPUT@
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34 -a $a
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35 -o chromatogram_library.elib
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36 && ls -l ./*.* inputs/*
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37 && cat chromatogram_library.elib.peptides.txt
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38 && cat chromatogram_library.elib.proteins.txt
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39 | tee -a search2lib.log
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40 ]]></command>
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41 <inputs>
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42 <expand macro="scan_inputs"/>
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43 <expand macro="lib_input" optional="false" libhelp="Use a Chromatogram elib from SearchToLib"/>
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44 <expand macro="fasta_input"/>
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45 <expand macro="target_fasta"/>
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46 <expand macro="options_section"/>
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47 <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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48 <param name="select_outputs" type="select" label="Select outputs" multiple="true">
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49 <option value="log" selected="true">log</option>
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50 <option value="elib" selected="true">elib</option>
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51 <option value="features" selected="false">concatenated_features.txt</option>
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52 <option value="results" selected="true">concatenated_results.txt</option>
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53 <option value="decoy" selected="false">concatenated_decoy.txt</option>
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54 <option value="rt_plots" selected="false">Retention Time Plots</option>
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55 <option value="rt_tables" selected="false">Retention Time Tables</option>
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56 <option value="peptides" selected="true">peptides.txt (requires align between files)</option>
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57 <option value="proteins" selected="true">proteins.txt (requires align between files)</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="search2lib.log">
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62 <filter>'log' in select_outputs</filter>
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63 </data>
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64 <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="chromatogram_library.elib">
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65 <filter>'elib' in select_outputs</filter>
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66 </data>
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67 <data name="features" format="tabular" label="${tool.name} ${on_string} concatenated_features.txt" from_work_dir="inputs/chromatogram_library_concatenated_features.txt">
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68 <filter>'features' in select_outputs</filter>
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69 <actions>
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70 <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,rank,peakZScore,peakCalibratedScore,deltaSn,avgIdotp,midIdotp,peakScore,peakWeightedScore,NCI,CIMassErrMean,CIMassErrVar,precursorMassErrMean,precursorMassErrVar,peakSimilarity,sampledTimes,midTime,spectraNorm,pepLength,charge2,charge3,precursorMz,sequence,protein" />
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71 </actions>
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72 </data>
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73 <data name="results" format="tabular" label="${tool.name} ${on_string} concatenated_results.txt" from_work_dir="inputs/chromatogram_library_concatenated_results.txt">
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74 <filter>'results' in select_outputs</filter>
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75 <actions>
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76 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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77 </actions>
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78 </data>
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79 <data name="decoy" format="tabular" label="${tool.name} ${on_string} concatenated_decoy.txt" from_work_dir="inputs/chromatogram_library_concatenated_decoy.txt">
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80 <filter>'decoy' in select_outputs</filter>
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81 <actions>
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82 <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
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83 </actions>
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84 </data>
3
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85 <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots">
5
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86 <filter>library and 'rt_plots' in select_outputs</filter>
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87 <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" directory="inputs"/>
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88 </collection>
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89 <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables">
5
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90 <filter>library and 'rt_tables' in select_outputs</filter>
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91 <discover_datasets pattern="(?P&lt;designation&gt;.+\.mzML\..+\.rt_fit\.txt)" ext="tabular" directory="inputs"/>
3
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92 </collection>
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93 <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt">
0
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94 <filter>a and 'peptides' in select_outputs</filter>
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95 <actions>
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96 <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" />
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97 </actions>
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98 </data>
3
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99 <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt">
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100 <filter>a and 'proteins' in select_outputs</filter>
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101 <actions>
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102 <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
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103 </actions>
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104 </data>
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105 </outputs>
4
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106 <tests>
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107 <test>
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108 <param name="scan_inputs" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML,BCS_hela_wide_500_900_2.mzML"/>
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109 <param name="library" ftype="elib" value="BCS_hela.elib"/>
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110 <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
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111 <output name="results" ftype="tabular">
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112 <assert_contents>
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113 <has_text text="GIEQAVQSHAVAEEEAR"/>
4
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114 </assert_contents>
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115 </output>
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116 <output name="peptides" ftype="tabular">
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117 <assert_contents>
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118 <has_text text="AYPLADAHLTK"/>
4
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119 </assert_contents>
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120 </output>
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121 </test>
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122 </tests>
0
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123 <help><![CDATA[
d3a6bc607825 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d0ac7888263b785e5aa039be6454d665b239e808-dirty"
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124
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125 **EncyclopeDIA Quantify**
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126
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127 @ENCYCLOPEDIA_WIKI@
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128
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129 EncyclopeDIA Quantify retention-time aligns peptides from the chromatogram library and produces quantitation results.
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130
5
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131
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132 **Inputs**
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133
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134 - Spectrum files in mzML format
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135 - A chromatogram library that can be generated by SearchToLib
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136 - A protein data base in fasta format
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137
0
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138 @MSCONVERT_HELP@
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139
5
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140 **Outputs**
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141
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142 - A log file
30f6b9c88ceb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"
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143 - A Chromatogram Library (.elib)
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144 - The identified features in tabular format
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145 Feature values of scans that are used by percolator to determine matches.
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146 - The identified Peptide Spectral Match results in tabular format
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147 Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
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148 - The identified peptides in tabular format
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149 Per peptide: the normalized intensity for each scan file.
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150 Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
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151 - The identified proteins in tabular format
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152 Per protein: the normalized intensity for each scan file.
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153 Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...
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154
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155
0
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156 **Typical DIA SearchToLib Workflow**
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157
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158 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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159
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160 1. SearchToLib is first run with the pooled narrow-window mzML files to create a combined DIA elib chromatogram library.
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161 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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162 Otherwise, SearchToLIB uses Walnut, a FASTA database search engine for DIA data that uses PECAN-style scoring.
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163
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164
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165 * 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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166
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167
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168 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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169
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170 .. image:: SearchToLib_Workflow.png
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171 :width: 810
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172 :height: 580
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173
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174 .. _Prosit: https://www.proteomicsdb.org/prosit
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175
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176 ]]></help>
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177 <expand macro="citations" />
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178 </tool>