Mercurial > repos > proteore > proteore_get_unique_peptide_srm_method
annotate proteore_get_unique_peptide_SRM-MRM_method.xml @ 1:b72ece649392 draft
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author | proteore |
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date | Thu, 30 Jan 2020 09:02:31 -0500 |
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1 <tool id="proteore_get_unique_peptide_srm_method" name="Get unique peptide SRM-MRM method" version="2020.01.30"> |
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2 <description>[Human SRM Atlas]</description> |
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3 <requirements> |
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4 </requirements> |
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5 <command detect_errors="exit_code"><![CDATA[ |
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6 |
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7 python $__tool_directory__/get_unique_srm.py |
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8 |
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9 #if $input.ids == "text" |
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10 --input="$input.txt" |
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11 --input_type="list" |
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12 #else |
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13 --input="$input.input_file" |
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14 --column_number="$input.ncol" |
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15 --header="$input.header" |
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16 --input_type="file" |
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17 #end if |
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18 |
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19 --features="$protein_features" |
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20 --output="$output" |
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21 |
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22 #if "SRM_atlas" in str($srm_file).split("/") |
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23 --ref_file="$srm_file" |
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24 #else |
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25 --ref_file="$__tool_directory__/$srm_file" |
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26 #end if |
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27 |
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28 ]]></command> |
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29 <inputs> |
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30 <conditional name="input" > |
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31 <param name="ids" type="select" label="Enter IDs (Uniprot Accession number, e.g. P04746)" help="Copy/paste or from a file (e.g. table)" > |
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32 <option value="text">Copy/paste your Uniprot-AC identifiers</option> |
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33 <option value="file" selected="true">Input file containing Uniprot-AC identifiers</option> |
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34 </param> |
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35 <when value="text" > |
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36 <param name="txt" type="text" label="Copy/paste IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' > |
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37 <sanitizer invalid_char=""> |
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38 <valid initial="string.printable"> |
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39 <remove value="'"/> |
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40 </valid> |
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41 <mapping initial="none"> |
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42 <add source="'" target="__sq__"/> |
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43 <add source=" " target=""/> |
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44 <add source="
" target=""/> |
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45 <add source="
" target=""/> |
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46 <add source="	" target=""/> |
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47 </mapping> |
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48 </sanitizer> |
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49 </param> |
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50 </when> |
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51 <when value="file" > |
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52 <param name="input_file" type="data" format="txt,tabular" label="Select your file" help="" /> |
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53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> |
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54 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> |
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55 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> |
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56 </param> |
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57 </when> |
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58 </conditional> |
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59 <param name="srm_file" type="select" label="Release" > |
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60 <options from_data_table="proteore_human_srm_atlas"> |
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61 <filter type="sort_by" column="0"/> |
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62 </options> |
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63 </param> |
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64 <param name="protein_features" type="select" label="Peptide sequence/features" multiple="true" help="" display="checkboxes" optional="false"> |
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65 <option value="PeptideSeq" selected="true">Peptide sequence</option> |
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66 <option value="SSRT" selected="false">SSRT (Sequence Specific Retention Time)</option> |
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67 <option value="Length" selected="false">Length (peptide sequence length)</option> |
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68 <option value="MW" selected="false">MW (Molecular weight)</option> |
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69 <option value="PA_AccNum" selected="false">PeptideAtlas Accession (PA_Acc)</option> |
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70 </param> |
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71 </inputs> |
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72 <outputs> |
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73 <data name="output" format="tsv"/> |
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74 </outputs> |
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75 <tests> |
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76 <test> |
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77 <conditional name="input" > |
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78 <param name="ids" value="file"/> |
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79 <param name="input_file" value="Lacombe_et_al_2017_modified.tsv" /> |
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80 <param name="header" value="true" /> |
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81 <param name="ncol" value="c1"/> |
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82 </conditional> |
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83 <param name="srm_file" value="tool-data/Human_SRM_atlas_2016-04.csv" /> |
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84 <param name="protein_features" value="PeptideSeq,SSRT,Length,MW,PA_AccNum"/> |
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85 <output name="output" value="srm_results.tsv" /> |
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86 </test> |
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87 </tests> |
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88 <help><![CDATA[ |
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89 **Description** |
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90 |
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91 This tool allows to retrieve unique proteotypic peptide and related information (from SRMAtlas) |
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92 for building Selected Reaction Monitoring (SRM) method using a list of Uniprot accession number as input. |
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93 The SRMAtlas is a compendium of targeted proteomics assays resulting from high-quality measurements of natural |
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94 and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource |
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95 for building selected/multiple reaction monitoring (SRM/MRM)-based proteomic methods. |
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96 |
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97 ----- |
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98 |
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99 **Input** |
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100 |
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101 A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing |
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102 the selected information (peptide sequence/features). If your input is a multiple-column file, the column(s) |
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103 containing the selected information will be added at the end of the input file. Only Uniprot accession number (e.g. P31946) are allowed. |
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104 If your list of IDs is not in this form, please use the ID_Converter tool of ProteoRE. |
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105 |
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106 .. class:: warningmark |
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107 |
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108 Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form. |
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109 |
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110 .. class:: warningmark |
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111 |
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112 In copy/paste mode, the number of IDs considered in input is limited to 5000. |
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113 |
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114 ----- |
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115 |
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116 **Parameters** |
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117 |
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118 Release: choose the release you want to use for retrieving peptide sequences/features |
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119 Peptide sequence/features: select peptide features you want to retrieve; Peptide sequence |
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120 (amino acid sequence of detected peptide, including any mass modifications); |
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121 SSRT (Sequence Specific Retention Time provides a hydrophobicity measure for each peptide using |
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122 the algorithm of Krohkin et al. SSRCalc); Length (peptide sequence length); MW (molecular weight); |
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123 PeptideAtlas Accession (PA_Acc). |
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124 |
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125 ----- |
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126 |
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127 **Output** |
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128 |
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129 A text file containing the selected peptide features (in addition to the original column(s) provided). |
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130 Please, note that a "NA" is returned when there is no match between a source ID and SRM/MRM source file. |
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131 |
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132 ----- |
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133 |
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134 **Data sources (release date)** |
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135 |
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136 This tool is using the following source file: |
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137 |
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138 - `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_. |
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139 |
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140 ----- |
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142 .. class:: infomark |
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144 **Authors** |
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146 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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147 |
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148 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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149 |
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150 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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152 Help: contact@proteore.org for any questions or concerns about this tool. |
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153 ]]></help> |
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154 </tool> |