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comparison proteore_get_unique_peptide_SRM-MRM_method.xml @ 0:a2b06836de90 draft
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author | proteore |
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date | Fri, 12 Jul 2019 07:49:45 -0400 |
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children | b72ece649392 |
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1 <tool id="proteore_get_unique_peptide_srm_method" name="Get unique peptide SRM-MRM method" version="2019.07.11"> | |
2 <description>[SRM Atlas]</description> | |
3 <requirements> | |
4 </requirements> | |
5 <command detect_errors="exit_code"><![CDATA[ | |
6 | |
7 python $__tool_directory__/get_unique_srm.py | |
8 | |
9 #if $input.ids == "text" | |
10 --input="$input.txt" | |
11 --input_type="list" | |
12 #else | |
13 --input="$input.input_file" | |
14 --column_number="$input.ncol" | |
15 --header="$input.header" | |
16 --input_type="file" | |
17 #end if | |
18 | |
19 --features="$protein_features" | |
20 --output="$output" | |
21 | |
22 #if "SRM_atlas" in str($srm_file).split("/") | |
23 --ref_file="$srm_file" | |
24 #else | |
25 --ref_file="$__tool_directory__/$srm_file" | |
26 #end if | |
27 | |
28 ]]></command> | |
29 <inputs> | |
30 <conditional name="input" > | |
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)" > | |
32 <option value="text">Copy/paste your Uniprot-AC identifiers</option> | |
33 <option value="file" selected="true">Input file containing Uniprot-AC identifiers</option> | |
34 </param> | |
35 <when value="text" > | |
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' > | |
37 <sanitizer invalid_char=""> | |
38 <valid initial="string.printable"> | |
39 <remove value="'"/> | |
40 </valid> | |
41 <mapping initial="none"> | |
42 <add source="'" target="__sq__"/> | |
43 <add source=" " target=""/> | |
44 <add source="
" target=""/> | |
45 <add source="
" target=""/> | |
46 <add source="	" target=""/> | |
47 </mapping> | |
48 </sanitizer> | |
49 </param> | |
50 </when> | |
51 <when value="file" > | |
52 <param name="input_file" type="data" format="txt,tabular" label="Select your file" help="" /> | |
53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> | |
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'> | |
55 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | |
56 </param> | |
57 </when> | |
58 </conditional> | |
59 <param name="srm_file" type="select" label="Release" > | |
60 <options from_data_table="proteore_human_srm_atlas"> | |
61 <filter type="sort_by" column="0"/> | |
62 </options> | |
63 </param> | |
64 <param name="protein_features" type="select" label="Peptide sequence/features" multiple="true" help="" display="checkboxes" optional="false"> | |
65 <option value="PeptideSeq" selected="true">Peptide sequence</option> | |
66 <option value="SSRT" selected="false">SSRT (Sequence Specific Retention Time)</option> | |
67 <option value="Length" selected="false">Length (peptide sequence length)</option> | |
68 <option value="MW" selected="false">MW (Molecular weight)</option> | |
69 <option value="PA_AccNum" selected="false">PeptideAtlas Accession (PA_Acc)</option> | |
70 </param> | |
71 </inputs> | |
72 <outputs> | |
73 <data name="output" format="tsv"/> | |
74 </outputs> | |
75 <tests> | |
76 <test> | |
77 <conditional name="input" > | |
78 <param name="ids" value="file"/> | |
79 <param name="input_file" value="Lacombe_et_al_2017_modified.tsv" /> | |
80 <param name="header" value="true" /> | |
81 <param name="ncol" value="c1"/> | |
82 </conditional> | |
83 <param name="srm_file" value="tool-data/Human_SRM_atlas_2016-04.csv" /> | |
84 <param name="protein_features" value="PeptideSeq,SSRT,Length,MW,PA_AccNum"/> | |
85 <output name="output" value="srm_results.tsv" /> | |
86 </test> | |
87 </tests> | |
88 <help><![CDATA[ | |
89 **Description** | |
90 | |
91 This tool allows to retrieve unique proteotypic peptide and related information (from SRMAtlas) | |
92 for building Selected Reaction Monitoring (SRM) method using a list of Uniprot accession number as input. | |
93 The SRMAtlas is a compendium of targeted proteomics assays resulting from high-quality measurements of natural | |
94 and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource | |
95 for building selected/multiple reaction monitoring (SRM/MRM)-based proteomic methods. | |
96 | |
97 ----- | |
98 | |
99 **Input** | |
100 | |
101 A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing | |
102 the selected information (peptide sequence/features). If your input is a multiple-column file, the column(s) | |
103 containing the selected information will be added at the end of the input file. Only Uniprot accession number (e.g. P31946) are allowed. | |
104 If your list of IDs is not in this form, please use the ID_Converter tool of ProteoRE. | |
105 | |
106 .. class:: warningmark | |
107 | |
108 Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form. | |
109 | |
110 .. class:: warningmark | |
111 | |
112 In copy/paste mode, the number of IDs considered in input is limited to 5000. | |
113 | |
114 ----- | |
115 | |
116 **Parameters** | |
117 | |
118 Release: choose the release you want to use for retrieving peptide sequences/features | |
119 Peptide sequence/features: select peptide features you want to retrieve; Peptide sequence | |
120 (amino acid sequence of detected peptide, including any mass modifications); | |
121 SSRT (Sequence Specific Retention Time provides a hydrophobicity measure for each peptide using | |
122 the algorithm of Krohkin et al. SSRCalc); Length (peptide sequence length); MW (molecular weight); | |
123 PeptideAtlas Accession (PA_Acc). | |
124 | |
125 ----- | |
126 | |
127 **Output** | |
128 | |
129 A text file containing the selected peptide features (in addition to the original column(s) provided). | |
130 Please, note that a "NA" is returned when there is no match between a source ID and SRM/MRM source file. | |
131 | |
132 ----- | |
133 | |
134 **Data sources (release date)** | |
135 | |
136 This tool is using the following source file: | |
137 | |
138 - `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_. | |
139 | |
140 ----- | |
141 | |
142 .. class:: infomark | |
143 | |
144 **Authors** | |
145 | |
146 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
147 | |
148 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR | |
149 | |
150 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
151 | |
152 Help: contact@proteore.org for any questions or concerns about this tool. | |
153 ]]></help> | |
154 </tool> |