Mercurial > repos > proteore > proteore_build_protein_interaction_maps
diff build_protein_interaction_maps.xml @ 2:99f6a94c1ade draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
| author | proteore |
|---|---|
| date | Fri, 28 Jun 2019 05:06:57 -0400 |
| parents | 0a85d709c4ae |
| children | 30dda8d454ce |
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--- a/build_protein_interaction_maps.xml Tue Mar 12 07:02:14 2019 -0400 +++ b/build_protein_interaction_maps.xml Fri Jun 28 05:06:57 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.03.12.2"> +<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.06.27"> <description>[BioGRID, BioPlex, HuMAP]</description> <requirements> </requirements> @@ -15,7 +15,7 @@ #end if --database=$database.ref #if $database.ref=="biogrid" - --species="${ filter( lambda x: str( x[3] ) == str( $database.ref_file ), $__app__.tool_data_tables['proteore_biogrid_dictionaries'].get_fields() )[0][2] }" + --species='$database.ref_file.fields.species' #else --species="Human" #end if @@ -77,7 +77,9 @@ <option value="GeneID" >Entrez gene ID</option> </param> <param name="ref_file" type="select" label="Species"> - <options from_data_table="proteore_biogrid_dictionaries" /> + <options from_data_table="proteore_biogrid_dictionaries"> + <filter type="sort_by" column="1"/> + </options> </param> </when> <when value="bioplex"> @@ -86,7 +88,9 @@ <option value="GeneID">Entrez gene ID</option> </param> <param name="ref_file" type="select" label="Species"> - <options from_data_table="proteore_bioplex_dictionaries" /> + <options from_data_table="proteore_bioplex_dictionaries"> + <filter type="sort_by" column="0"/> + </options> </param> </when> <when value="humap"> @@ -94,7 +98,9 @@ <option value="GeneID" >Entrez gene ID</option> </param> <param name="ref_file" type="select" label="Species"> - <options from_data_table="proteore_humap_dictionaries" /> + <options from_data_table="proteore_humap_dictionaries"> + <filter type="sort_by" column="0"/> + </options> </param> </when> </conditional> @@ -113,6 +119,83 @@ <filter>input['ids'] == "file"</filter> </data> </outputs> + <tests> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Lacombe_geneID.tsv" /> + <param name="header" value="true" /> + <param name="ncol" value="c1"/> + </conditional> + <conditional name="database"> + <param name="ref" value="bioplex"/> + <param name="id_type" value="UniProt-AC"/> + <param name="ref_file" value="tool-data/Human_bioplex_2019-03-01"/> + </conditional> + <output name="network_output" value="Network_bioplex_from_Lacombe_geneID.tsv"/> + <output name="nodes_output" value="Nodes_bioplex_from_Lacombe_geneID.tsv"/> + </test> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Lacombe_geneID.tsv" /> + <param name="header" value="true" /> + <param name="ncol" value="c4"/> + </conditional> + <conditional name="database"> + <param name="ref" value="humap"/> + <param name="id_type" value="GeneID"/> + <param name="ref_file" value="tool-data/Human_humap_2019-03-01"/> + </conditional> + <output name="network_output" value="Network_humap_from_Lacombe_geneID.tsv"/> + <output name="nodes_output" value="Nodes_humap_from_Lacombe_geneID.tsv"/> + </test> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Lacombe_geneID.tsv" /> + <param name="header" value="true" /> + <param name="ncol" value="c4"/> + </conditional> + <conditional name="database"> + <param name="ref" value="biogrid"/> + <param name="id_type" value="GeneID"/> + <param name="ref_file" value="tool-data/Human_biogrid_2019-03-01"/> + </conditional> + <output name="network_output" value="Network_biogrid_from_Lacombe_geneID.tsv"/> + <output name="nodes_output" value="Nodes_biogrid_from_Lacombe_geneID.tsv"/> + </test> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Wilson-foie-souris-up_geneID.tsv" /> + <param name="header" value="true" /> + <param name="ncol" value="c2"/> + </conditional> + <conditional name="database"> + <param name="ref" value="biogrid"/> + <param name="id_type" value="GeneID"/> + <param name="ref_file" value="tool-data/Mouse_biogrid_2019-03-01"/> + </conditional> + <output name="network_output" value="Network_biogrid_from_Wilson-foie-souris_geneID.tsv"/> + <output name="nodes_output" value="Nodes_biogrid_from_Wilson-foie-souris_geneID.tsv"/> + </test> + <test> + <conditional name="input"> + <param name="ids" value="file"/> + <param name="file" value="Rattus_Hameza_dataset_geneID.tsv" /> + <param name="header" value="true" /> + <param name="ncol" value="c4"/> + </conditional> + <conditional name="database"> + <param name="ref" value="biogrid"/> + <param name="id_type" value="GeneID"/> + <param name="ref_file" value="tool-data/Rat_biogrid_2019-03-01"/> + </conditional> + <output name="network_output" value="Network_biogrid_from_Rattus_Hameza_dataset_geneID.tsv"/> + <output name="nodes_output" value="Nodes_biogrid_from_Rattus_Hameza_dataset_geneID.tsv"/> + </test> + </tests> <help><![CDATA[ **Description** @@ -124,6 +207,10 @@ "Enter IDs": A list of IDs must be entered either via a copy/paste or by choosing a file. The type of identifiers allowed depends on the public resource you select (see below). +.. class:: warningmark + +In copy/paste mode, the number of IDs considered in input is limited to 5000. + ----- **Parameters** @@ -179,13 +266,17 @@ .. class:: infomark **Data source (release date)** + This tool uses the following public ressources: - **BioGRID**: 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: + BIOGRID-ORGANISM-Homo_sapiens-3.5.167.tab2.txt + BIOGRID-ORGANISM-Mus_musculus-3.5.167.tab2.txt + BIOGRID-ORGANISM-Rattus_norvegicus-3.5.167.tab2.txt - **Bioplex**: Version 2.0 @@ -195,6 +286,7 @@ - **Human protein complex Map (Hu.map)**: nodeTable.txt: http://proteincomplexes.org/static/downloads/nodeTable.txt + pairsWprob: http://proteincomplexes.org/static/downloads/pairsWprob.txt Mapping files linking the source database identifier (Entrez gene ID and Uniprot Accession Number) to the Reactome pathways are based on 2018-12-07 version, NCBI2Reactome.txt and UniProt2Reactome.txt (from https://www.reactome.org/download-data). @@ -211,7 +303,7 @@ This work has been partially funded through the French National Agency for Research (ANR) IFB project. -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. +Help: contact@proteore.org for any questions or concerns about the Galaxy implementation of this tool. ]]></help> <citations> </citations>