Mercurial > repos > proteore > proteore_build_protein_interaction_maps
comparison build_protein_interaction_maps.xml @ 5:ba96ca3496a2 draft default tip
"planemo upload commit c9a32e920aae2bc186183611bc0abb2040e106f3"
author | proteore |
---|---|
date | Thu, 06 Feb 2020 08:28:04 -0500 |
parents | 4db07f536a32 |
children |
comparison
equal
deleted
inserted
replaced
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 |