comparison build_protein_interaction_maps.xml @ 2:99f6a94c1ade draft

planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

1:0a85d709c4ae

<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.03.12.2">
<description>[BioGRID, BioPlex, HuMAP]</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/build_protein_interaction_maps.py 

                --header="$input.header"
                --input_type="file"
            #end if
            --database=$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] }"
            #else 
                --species="Human"
            #end if

            #if 'PPI_dictionaries' in str($database.ref_file).split('/') : 

            <when value="biogrid">
                <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
                    <option value="GeneID" >Entrez gene ID</option>
                </param>
                <param name="ref_file" type="select" label="Species">
                    <options from_data_table="proteore_biogrid_dictionaries" />
                </param>
            </when>
            <when value="bioplex">
                <param name="id_type" type="select" label="Type/source of IDs" optional="false">
                    <option value="UniProt-AC" selected="True" >UniProt accession number</option>
                    <option value="GeneID">Entrez gene ID</option>
                </param>
                <param name="ref_file" type="select" label="Species">
                    <options from_data_table="proteore_bioplex_dictionaries" />
                </param>
            </when>
            <when value="humap">
                <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
                    <option value="GeneID" >Entrez gene ID</option>
                </param>
                <param name="ref_file" type="select" label="Species">
                    <options from_data_table="proteore_humap_dictionaries" />
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>

        </data>
        <data name="nodes_output" format="tsv" label="Nodes_${database.ref}_from_${input.file.name}">
            <filter>input['ids'] == "file"</filter>
        </data>
    </outputs>
    <help><![CDATA[
**Description**

As elementary constituents of cellular protein complexes and pathways, protein–protein interactions (PPIs) are key determinants of protein function. This tool allows building interaction maps by mapping your list of protein or gene identifiers on different public resources; indeed, according to your need and the species of interest, different PPIs resources are available (for details see “Parameters” section). The two result files generated (network and nodes attributes) can be used for viewing and further exploration of the resulting protein interactions network by directly importing those in dedicated software (e.g. Cytoscape).   

-----

**Input**

"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).  

-----

**Parameters**

-----

.. 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 

BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv

- **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).

-----

Sandra Dérozier, Olivier Rué, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR

This work has been partially funded through the French National Agency for Research (ANR) IFB project.

Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
    ]]></help>
    <citations>
    </citations>
 </tool>

2:99f6a94c1ade

<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.06.27">
<description>[BioGRID, BioPlex, HuMAP]</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/build_protein_interaction_maps.py 

                --header="$input.header"
                --input_type="file"
            #end if
            --database=$database.ref
            #if $database.ref=="biogrid" 
                --species='$database.ref_file.fields.species'
            #else 
                --species="Human"
            #end if

            #if 'PPI_dictionaries' in str($database.ref_file).split('/') : 

            <when value="biogrid">
                <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
                    <option value="GeneID" >Entrez gene ID</option>
                </param>
                <param name="ref_file" type="select" label="Species">
                    <options from_data_table="proteore_biogrid_dictionaries">
                        <filter type="sort_by" column="1"/>
                    </options>
                </param>
            </when>
            <when value="bioplex">
                <param name="id_type" type="select" label="Type/source of IDs" optional="false">
                    <option value="UniProt-AC" selected="True" >UniProt accession number</option>
                    <option value="GeneID">Entrez gene ID</option>
                </param>
                <param name="ref_file" type="select" label="Species">
                    <options from_data_table="proteore_bioplex_dictionaries">
                        <filter type="sort_by" column="0"/>
                    </options>
                </param>
            </when>
            <when value="humap">
                <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
                    <option value="GeneID" >Entrez gene ID</option>
                </param>
                <param name="ref_file" type="select" label="Species">
                    <options from_data_table="proteore_humap_dictionaries">
                        <filter type="sort_by" column="0"/>
                    </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>

        </data>
        <data name="nodes_output" format="tsv" label="Nodes_${database.ref}_from_${input.file.name}">
            <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**

As elementary constituents of cellular protein complexes and pathways, protein–protein interactions (PPIs) are key determinants of protein function. This tool allows building interaction maps by mapping your list of protein or gene identifiers on different public resources; indeed, according to your need and the species of interest, different PPIs resources are available (for details see “Parameters” section). The two result files generated (network and nodes attributes) can be used for viewing and further exploration of the resulting protein interactions network by directly importing those in dedicated software (e.g. Cytoscape).   

-----

**Input**

"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**

-----

.. 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 

BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv

- **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).

-----

Sandra Dérozier, Olivier Rué, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR

This work has been partially funded through the French National Agency for Research (ANR) IFB project.

Help: [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
    ]]></help>
    <citations>
    </citations>
 </tool>