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comparison add_protein_features.xml @ 16:7caa90759aba draft

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planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:05:25 -0400
parents da885fff7cf6
children 2952bae8a1ea
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15:da885fff7cf6 16:7caa90759aba
1 <tool id="prot_features" name="Add protein features" version="2019.05.06"> 1 <tool id="prot_features" name="Add protein features" version="2019.06.27.2">
2 <description>[neXtProt] 2 <description>[neXtProt]
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>
32 32
33 ]]></command> 33 ]]></command>
34 34
35 <inputs> 35 <inputs>
36 <conditional name="inputtype"> 36 <conditional name="inputtype">
37 <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" help="Copy/paste or from a file" > 37 <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt; e.g. P05090 or NX_P05090)" help="Copy/paste or from a file" >
38 <option value="file" selected="true">Input file containing your IDs </option> 38 <option value="file" selected="true">Input file containing your IDs </option>
39 <option value="copy_paste">Copy/paste your list of IDs</option> 39 <option value="copy_paste">Copy/paste your list of IDs</option>
40 </param> 40 </param>
41 <when value="copy_paste"> 41 <when value="copy_paste">
42 <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0"> 42 <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0">
62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" /> 62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
63 </when> 63 </when>
64 </conditional> 64 </conditional>
65 65
66 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> 66 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false">
67 <option value="Uniprot_AC" selected="true">Uniprot accession number</option> 67 <option value="NextprotID" selected="true">neXtProt IDs</option>
68 <option value="NextprotID" selected="false">neXtProt IDs</option> 68 <option value="Uniprot_AC" selected="false">UniProt accession number</option>
69 </param> 69 </param>
70 <section name="Nextprot_params" title="Select features" expanded="True"> 70 <section name="Nextprot_params" title="Select features (Physico-chemical, localization, disease infiormation)" expanded="True">
71 <param name="pc_features" type="select" label="Physico-Chemical Features" 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">
72 <option value="SeqLength" selected="false">Sequence Length</option> 72 <option value="SeqLength" selected="false">Sequence Length</option>
73 <option value="MW" selected="false">Molecular Weight</option> 73 <option value="MW" selected="false">Molecular Weight</option>
74 <option value="IsoPoint" selected="false">Isoelectric point</option> 74 <option value="IsoPoint" selected="false">Isoelectric point</option>
75 <option value="TMDomains" selected="false">Number of transmembrane domains</option> 75 <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> 76 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
77 </param>
78
79 <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true">
80 <option value="Chr" selected="false">Chromosome</option>
81 <option value="SubcellLocations" selected="false">Subcellular Location</option>
77 </param> 82 </param>
78 83
79 <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> 84 <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" />
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="false" truevalue="true" falsevalue="false" label="Disease information" />
85 85
86 </section> 86 </section>
87 <param name="ref_file" type="select" label="Release of neXtProt reference file to use"> 87 <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
88 <options from_data_table="proteore_nextprot_ref"/> 88 <options from_data_table="proteore_nextprot_ref">
89 <filter type="sort_by" column="0"/>
90 </options>
89 </param> 91 </param>
90 92
91 </inputs> 93 </inputs>
92 94
93 95
99 </outputs> 101 </outputs>
100 102
101 <tests> 103 <tests>
102 <test> 104 <test>
103 <conditional name="inputtype"> 105 <conditional name="inputtype">
104 <param name="filetype " value="file"/> 106 <param name="filetype" value="file"/>
105 <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv"/> 107 <param name="genelist" value="Lacombe_et_al_2017.tsv"/>
106 <param name="column" value="c1"/> 108 <param name="column" value="c1"/>
107 <param name="header" value="true"/> 109 <param name="header" value="true"/>
108 </conditional> 110 </conditional>
109 111
110 <param name="idtype" value="uniprot"/> 112 <param name="idtype" value="Uniprot_AC"/>
111 113
112 <section name="Nextprot_params"> 114 <section name="Nextprot_params">
113 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> 115 <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/>
114 <param name="localization" value="Chr,SubcellLocations"/> 116 <param name="localization" value="Chr,SubcellLocations"/>
115 <param name="diseases_info" value="true"/> 117 <param name="diseases_info" value="true"/>
116 </section> 118 </section>
117 119
120 <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/>
118 <output name="output" file="Add_information_from_neXtProt.tsv"/> 121 <output name="output" file="Add_information_from_neXtProt.tsv"/>
119 </test> 122 </test>
120 </tests> 123 </tests>
121 124
122 <help><![CDATA[ 125 <help><![CDATA[
129 132
130 **Input** 133 **Input**
131 134
132 A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool. 135 A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool.
133 136
137 .. class:: warningmark
138
139 In copy/paste mode, the number of IDs considered in input is limited to 5000.
140
134 ----- 141 -----
135 142
136 **Parameters** 143 **Parameters**
137 144
138 "Select features": three categories of annotation can be retrieved: physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. 145 "Select features": select each feature of your interest by clicking the corresponding checkbox. Disease information is set to "Yes" by default.
139 146
140 ----- 147 -----
141 148
142 **Output** 149 **Output**
143 150
145 152
146 ----- 153 -----
147 154
148 **Data source (release date)** 155 **Data source (release date)**
149 156
150 Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release January 2018) 157 Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017)
151 158
152 using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et al., 2017) 159 neXtProt releases :
153 160
161 - nextProt release 07-05-2019 (release Feb 13, 2019)
162 - neXtProt release 08-10-2018 (release Feb 21, 2018)
163
154 ----- 164 -----
155 165
156 .. class:: infomark 166 .. class:: infomark
157 167
158 **Authors** 168 **Authors**
161 171
162 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 172 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
163 173
164 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 174 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
165 175
166 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 176 Help: contact@proteore.org for any questions or concerns about this tool.
167 177
168 ]]></help> 178 ]]></help>
169 <citations> 179 <citations>
170 </citations> 180 </citations>
171 181