Mercurial > repos > proteore > proteore_prot_features
comparison add_protein_features.xml @ 18:0a9ae3d7dbf2 draft default tip
"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7"
author | proteore |
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date | Thu, 20 Aug 2020 03:09:52 -0400 |
parents | 2952bae8a1ea |
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17:2952bae8a1ea | 18:0a9ae3d7dbf2 |
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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 |