annotate README.rst @ 6:c1364679388d draft

planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty

Wrapper for ID Converter tool
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**Authors**

T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR

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

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.

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This tool converts a list of IDs to another identifier type, select the source and target type from the dropdown menus above (see below supported source and target types).

After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to. 

If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs. Please, note that a "NA" is returned when there is no corresponding ID.

If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.

**Available databases**

* neXtProt ID (e.g. NX_P31946)

* Uniprot accession number (e.g. P31946)

* Uniprot ID (e.g 1433B_HUMAN)

* Entrez gene ID (e.g. 7529)

* RefSeq (NCBI) protein (e.g.  NP_003395.1)

* GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)

* Protein DataBank ID (e.g. 2BR9:A)

* GOterms (Gene Ontology) ID (e.g. GO:0070062)

* Protein Information Resource ID (e.g. S34755)

* OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)

* Unigene ID (e.g. Hs.643544)

* Ensembl gene ID (e.g. ENSG00000166913)

* Ensembl transcript ID (e.g. ENST00000353703)

* Ensembl protein ID (e.g. ENSP00000300161)

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.. class:: infomark

This tool converts human IDs using the following source files:

* HUMAN_9606_idmapping_selected.tab (Uniprot released on 12/2017)
    Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/

* nextprot_ac_list_all.txt (Nextprot released on 01/08/2017)
    Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/

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.. class:: warningmark

Accession numbers with an hyphen ("-") that normally correspond to isoform are considered 
(and will therefore be treated) as similar to its canonical form.

For example, "Q71U36-2" will be treated as "Q71U36".