comparison build_protein_interaction_maps.xml @ 1:0a85d709c4ae draft

planemo upload commit 567ba7934c0ca55529dfeb5e7ca0935ace260ad7-dirty

0:b0ac71686b99

<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.03.08">
<description>[BioGRID, BioPlex, HuMAP]</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/build_protein_interaction_maps.py 

Two output files are created with the follwing prefix "Network_PPIdatabaseName\_" and a "Nodes_PPIdatabaseName\_" (where "PPIdatabaseName" correspond to the PPI database selected). 
The "Network" file contains information related to each interaction between two proteins (one row per binary interaction) while the "Nodes" file contains attributes (i.e. annotation, information) related to each gene/protein.
Below is shown a brief example of each output file when BioGRID is selected. Note that a "NA" is added when there is no available information.

.. csv-table:: Network file (if BioGRID database selected - simulated data)
   :header: "Entrez_Gene_Interactor_A","Entrez Gene Interactor B","Gene symbol Interactor A","Gene symbol Interactor B","Experimental System","Experimental Type","Pubmed ID","Interaction Score","Phenotypes"

    1,368,"A1BG","ABCC6","Two-hybrid","physical",21988832,"NA","Growth abnormality"
    1,10549,"A1BG","PRDX4","Negative Genetic","genetic",21988832,"NA","NA"
    1,9923,"A1BG","ZBTB40","Affinity Capture-MS","physical",28514442,0.99977983,"NA"  


**"Interaction Score"**: a positive for negative value recorded by the original publication depicting P-Values, Confidence Score, SGA Score, etc. Will be “NA” if no score is reported.

.. csv-table:: Nodes file (if BioGRID database selected - simulated data)
   :header: "Entrez gene ID","Official Symbol Interactor","Present in user input ids","ID present in Biogrid Human","Pathway"
   
	"1","A1BG","True","True","Platelet degranulation ;Neutrophil degranulation"

.. class:: infomark

**Galaxy integration**

David Christiany, Lisa Perus, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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>

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 

Two output files are created with the follwing prefix "Network_PPIdatabaseName\_" and a "Nodes_PPIdatabaseName\_" (where "PPIdatabaseName" correspond to the PPI database selected). 
The "Network" file contains information related to each interaction between two proteins (one row per binary interaction) while the "Nodes" file contains attributes (i.e. annotation, information) related to each gene/protein.
Below is shown a brief example of each output file when BioGRID is selected. Note that a "NA" is added when there is no available information.

"Network" output file (example): 

.. csv-table:: Network file (if BioGRID database selected - simulated data)
   :header: "Entrez_Gene_Interactor_A","Entrez Gene Interactor B","Gene symbol Interactor A","Gene symbol Interactor B","Experimental System","Experimental Type","Pubmed ID","Interaction Score","Phenotypes"

    1,368,"A1BG","ABCC6","Two-hybrid","physical",21988832,"NA","Growth abnormality"
    1,10549,"A1BG","PRDX4","Negative Genetic","genetic",21988832,"NA","NA"
    1,9923,"A1BG","ZBTB40","Affinity Capture-MS","physical",28514442,0.99977983,"NA"  


**"Interaction Score"**: a positive for negative value recorded by the original publication depicting P-Values, Confidence Score, SGA Score, etc. Will be “NA” if no score is reported.

"Nodes" output file (example):

.. csv-table:: Nodes file (if BioGRID database selected - simulated data)
   :header: "Entrez gene ID","Official Symbol Interactor","Present in user input ids","ID present in Biogrid Human","Pathway"
   
	"1","A1BG","True","True","Platelet degranulation ;Neutrophil degranulation"

.. class:: infomark

**Galaxy integration**

David Christiany, Lisa Perus, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR

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>