Mercurial > repos > proteore > proteore_prot_features

comparison add_protein_features.xml @ 18:0a9ae3d7dbf2 draft default tip

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"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7"
author proteore
date Thu, 20 Aug 2020 03:09:52 -0400
parents 2952bae8a1ea
children
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17:2952bae8a1ea 18:0a9ae3d7dbf2
1 <tool id="prot_features" name="Add protein features" version="2020.01.23"> 1 <tool id="prot_features" name="Add protein features" version="2020.08.17">
2 <description>[neXtProt, Human] 2 <description>[neXtProt, Human]
3 </description> 3 </description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.4.1">R</requirement> 5 <requirement type="package" version="3.4.1">R</requirement>
6 </requirements> 6 </requirements>
17 --column='$inputtype.column' 17 --column='$inputtype.column'
18 --header=$inputtype.header 18 --header=$inputtype.header
19 #end if 19 #end if
20 20
21 --type='$idtype' 21 --type='$idtype'
22 --pc_features='$Nextprot_params.pc_features' 22 --pc_features='$pc_features'
23 --localization='$Nextprot_params.localization'
24 --diseases_info='$Nextprot_params.diseases_info'
25 --output='$output' 23 --output='$output'
26 24
27 #if 'proteore_nextprot_ref' in str($ref_file).split("/") 25 #if 'proteore_nextprot_ref' in str($ref_file).split("/")
28 --nextprot="$ref_file" 26 --nextprot="$ref_file"
29 #else 27 #else
61 </param> 59 </param>
62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" /> 60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
63 </when> 61 </when>
64 </conditional> 62 </conditional>
65 63
66 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> 64 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false">
67 <option value="NextprotID" selected="true">neXtProt IDs</option> 65 <option value="NextprotID" selected="true">neXtProt IDs</option>
68 <option value="Uniprot_AC" selected="false">UniProt accession number</option> 66 <option value="Uniprot_AC" selected="false">UniProt accession number</option>
69 </param> 67 </param>
70 <section name="Nextprot_params" title="Select features (Physico-chemical, localization, disease infiormation)" expanded="True"> 68 <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
71 <param name="pc_features" type="select" label="Select information to add to your list" multiple="true" help="" display="checkboxes" optional="false"> 69 <option value="ProteinName" selected="false">Protein name</option>
72 <option value="SeqLength" selected="false">Sequence Length</option> 70 <option value="SeqLength" selected="false">Sequence Length</option>
73 <option value="MW" selected="false">Molecular Weight</option> 71 <option value="MW" selected="false">Molecular Weight</option>
74 <option value="IsoPoint" selected="false">Isoelectric point</option> 72 <option value="IsoPoint" selected="false">Isoelectric point</option>
75 <option value="TMDomains" selected="false">Number of transmembrane domains</option> 73 <option value="TMDomains" selected="false">Number of transmembrane domains</option>
76 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> 74 <option value="SubcellLocations" selected="false">Subcellular Location</option>
77 </param> 75 <option value="Diseases" selected="false">Disease information</option>
76 <option value="Function" selected="false">Protein function</option>
77 <option value="PostTranslationalModifications" selected="false">Post translational modifications</option>
78 <option value="ProteinFamily" selected="false">Protein family</option>
79 <option value="Pathway" selected="false">Pathway(s)</option>
80 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
81 <option value="Chr" selected="false">Chromosome</option>
82 </param>
78 83
79 <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> 84 <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
80 <option value="Chr" selected="false">Chromosome</option>
81 <option value="SubcellLocations" selected="false">Subcellular Location</option>
82 </param>
83
84 <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" />
85
86 </section>
87 <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
88 <options from_data_table="proteore_nextprot_ref"> 85 <options from_data_table="proteore_nextprot_ref">
89 <filter type="sort_by" column="0"/> 86 <filter type="sort_by" column="0"/>
90 </options> 87 </options>
91 </param> 88 </param>
92 89
93 </inputs> 90 </inputs>
94 91
95 92
96 <outputs> 93 <outputs>
108 <param name="column" value="c1"/> 105 <param name="column" value="c1"/>
109 <param name="header" value="true"/> 106 <param name="header" value="true"/>
110 </conditional> 107 </conditional>
111 108
112 <param name="idtype" value="Uniprot_AC"/> 109 <param name="idtype" value="Uniprot_AC"/>
113 110 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/>
114 <section name="Nextprot_params">
115 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/>
116 <param name="localization" value="Chr,SubcellLocations"/>
117 <param name="diseases_info" value="true"/>
118 </section>
119 111
120 <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/> 112 <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/>
121 <output name="output" file="Add_information_from_neXtProt.tsv"/> 113 <output name="output" file="Add_information_from_neXtProt.tsv"/>
122 </test> 114 </test>
123 </tests> 115 </tests>
124 116
125 <help><![CDATA[ 117 <help><![CDATA[
126 118
127 **Description** 119 **Description**
128 120
129 This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list. 121 This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich and better inform your protein IDs list.
130 122
131 ----- 123 -----
132 124
133 **Input** 125 **Input**
134 126
146 138
147 ----- 139 -----
148 140
149 **Output** 141 **Output**
150 142
151 Output is a tabular file containing both original columns and new columns including the annotation requested. 143 Output is a tabular file containing both original columns and new columns including the annotation requested. Only features/annotations assigned with a "GOLD" quality criterion are considered, otherwise a "NA" value is returned.
144
145 .. class:: warningmark
146
147 "Protein name","Protein function","Post translational modifications","Protein family","Pathway(s)" options will not work will releases older than 08/2020.
152 148
153 ----- 149 -----
154 150
155 **Data source (release date)** 151 **Data source (release date)**
156 152
157 Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017) 153 Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017)
158 154
159 neXtProt releases : 155 neXtProt releases :
160 156
161 - nextProt release 07-05-2019 (release Feb 13, 2019) 157 - nextProt release 31-07-2020 (release Feb, 2020)
162 - neXtProt release 08-10-2018 (release Feb 21, 2018) 158 - nextProt release 07-05-2019 (release Feb, 2019)
159 - neXtProt release 08-10-2018 (release Feb, 2018)
163 160
161 .. class:: warningmark
162
163 For "Protein function", "Post translational modifications" and "Pathway(s)", only results with gold quality are returned.
164
164 ----- 165 -----
165 166
166 .. class:: infomark 167 .. class:: infomark
167 168
168 **Authors** 169 **Authors**
169 170
170 David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 171 David Christiany, Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
171 172
172 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 173 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
173 174
174 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 175 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
175 176