Mercurial > repos > proteore > proteore_build_protein_interaction_maps

comparison build_protein_interaction_maps.xml @ 5:ba96ca3496a2 draft default tip

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"planemo upload commit c9a32e920aae2bc186183611bc0abb2040e106f3"
author proteore
date Thu, 06 Feb 2020 08:28:04 -0500
parents 4db07f536a32
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4:4db07f536a32 5:ba96ca3496a2
1 <tool id="build_protein_interaction_maps" name="Build Protein interaction network" version="2020.01.23"> 1 <tool id="build_protein_interaction_maps" name="Build Protein interaction network" version="2020.02.06">
2 <description>[BioGRID, BioPlex, HuMAP]</description> 2 <description>[BioGRID, BioPlex, HuMAP]</description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 python $__tool_directory__/build_protein_interaction_maps.py 6 python $__tool_directory__/build_protein_interaction_maps.py
74 </param> 74 </param>
75 <when value="biogrid"> 75 <when value="biogrid">
76 <param name="id_type" type="select" label="Type/source of IDs" optional="false" > 76 <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
77 <option value="GeneID" >Entrez gene ID</option> 77 <option value="GeneID" >Entrez gene ID</option>
78 </param> 78 </param>
79 <param name="ref_file" type="select" label="Species"> 79 <param name="ref_file" type="select" label="Species and release date">
80 <options from_data_table="proteore_biogrid_dictionaries"> 80 <options from_data_table="proteore_biogrid_dictionaries">
81 <filter type="sort_by" column="1"/> 81 <filter type="sort_by" column="1"/>
82 </options> 82 </options>
83 </param> 83 </param>
84 </when> 84 </when>
85 <when value="bioplex"> 85 <when value="bioplex">
86 <param name="id_type" type="select" label="Type/source of IDs" optional="false"> 86 <param name="id_type" type="select" label="Type/source of IDs" optional="false">
87 <option value="UniProt-AC" selected="True" >UniProt accession number</option> 87 <option value="UniProt-AC" selected="True" >UniProt accession number</option>
88 <option value="GeneID">Entrez gene ID</option> 88 <option value="GeneID">Entrez gene ID</option>
89 </param> 89 </param>
90 <param name="ref_file" type="select" label="Species"> 90 <param name="ref_file" type="select" label="Species and release date">
91 <options from_data_table="proteore_bioplex_dictionaries"> 91 <options from_data_table="proteore_bioplex_dictionaries">
92 <filter type="sort_by" column="0"/> 92 <filter type="sort_by" column="0"/>
93 </options> 93 </options>
94 </param> 94 </param>
95 </when> 95 </when>
265 265
266 .. class:: infomark 266 .. class:: infomark
267 267
268 **Data source (release date)** 268 **Data source (release date)**
269 269
270 This tool uses the following public ressources: 270 This tool uses the following public ressources (for more details please check: http://www.proteore.org/static/data_source.html)
271 271
272 - **BioGRID**: 272 - **BioGRID**:
273 273
274 The release 3.5.167 was compiled on Nov. 25rd, 2018 and contains all curated interaction data processed prior to this date. Source files are: 274 Data were downloaded from BioGrid: https://downloads.thebiogrid.org/BioGRID/
275 275
276 BIOGRID-ORGANISM-Homo_sapiens-3.5.167.tab2.txt 276 Installation date:
277 277
278 BIOGRID-ORGANISM-Mus_musculus-3.5.167.tab2.txt 278 06/02/2020
279 279
280 BIOGRID-ORGANISM-Rattus_norvegicus-3.5.167.tab2.txt 280 01/03/2019
281
281 282
282 - **Bioplex**: Version 2.0 283 - **Bioplex**: Version 2.0
283 284
284 BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv 285 BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv
285 286