comparison id_converter.xml @ 15:b50d913ec067 draft

planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b

14:659f1248f535

<tool id="IDconverter" name="ID Converter" version="2018.09.18">
    <description>convert public database identifiers
    </description>
    <requirements>
      <requirement type="package" version="3.4.1">R</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript">
        $__tool_directory__/id_converter_UniProt.R
        --id_type="$species.idtypein"
        #if $input.ids == "text"
            --input="$input.txt"
            --input_type="list"
        #else

            --header="$input.header"
            --input_type="file"
        #end if
        --target_ids="$species.idto.idtypeout"
        --output="$output"
        --ref_file="$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables['id_mapping_tab'].get_fields() )[0][-1] }"
        
    </command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
                <option value="text">Copy/paste your identifiers</option>
                <option value="file" selected="true">Input file containing your identifiers</option>
            </param>
            <when value="text" >
                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
                    <sanitizer invalid_char="">
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping initial="none">

                        </mapping>
                    </sanitizer>
                </param>
            </when>
            <when value="file" >
                <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
            </when>
        </conditional>
        <conditional name="species">
            <param name="mapping_file" type="select" label="Select species for ID conversion" >
                <options from_data_table="id_mapping_tab"/>
                <option value="human_id_mapping"></option>
                <option value="mouse_id_mapping"></option>
            </param>
            <when value="human_id_mapping">
                <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
                    <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                    <option value="UniProt.AC" selected="True" >Uniprot accession number (e.g. P31946)</option>
                    <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                    <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
                    <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                    <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
                </param>
                <section name="idto" title="Target type of IDs" expanded="True" >
                    <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" help="Please see example of IDs in help section" >
                        <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                        <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option>
                        <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
                        <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                        <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                        <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                        <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="mouse_id_mapping">
                <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
                    <option value="UniProt.AC" selected="True" >Uniprot accession number (e.g. P31946)</option>
                    <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                    <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
                    <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                    <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
                </param>
                <section name="idto" title="Target type of IDs" expanded="True" >
                    <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" help="Please see example of IDs in help section" >
                        <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option>
                        <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option>
                        <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                        <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                        <option value="GI" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option>
                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                        <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <conditional name="input" >
                <param name="ids" value="file"/>

                <param name="header" value="true" />
                <param name="ncol" value="c1"/>
            </conditional>
            <conditional name="species">
                <param name="mapping_file" value="human_id_mapping"/>
                <param name="idtypein" value="UniProt.AC"/>
                <section name="idto">
                    <param name="idtypeout" value="neXtProt,UniProt.ID,GeneID,MIM,Ensembl" />
                </section>
            </conditional>
            <output name="output" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
        </test>
    </tests>
    <help><![CDATA[
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)

* Ensembl transcript ID (e.g. ENST00000353703)

* Ensembl protein ID (e.g. ENSP00000300161)

-----

.. class:: infomark

This tool converts human IDs using the following source files:

* HUMAN_9606_idmapping_selected.tab (Uniprot 02/07/2018)
    Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/

* HUMAN_9606_idmapping.dat (Uniprot 02/07/18)
    Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/

* nextprot_ac_list_all.txt (Nextprot released on 17/01/2018)
    Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/

-----

.. 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".

-----

.. class:: infomark

**Authors**

T.P. Lien Nguyen, David Christiany, 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.
 

15:b50d913ec067

<tool id="IDconverter" name="ID Converter" version="2018.12.18">
    <description>(Human, Mouse, Rat)
    </description>
    <requirements>
      <requirement type="package" version="3.4.1">R</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript">
        $__tool_directory__/id_converter.R
        --id_type="$species.idtypein"
        #if $input.ids == "text"
            --input="$input.txt"
            --input_type="list"
        #else

            --header="$input.header"
            --input_type="file"
        #end if
        --target_ids="$species.idto.idtypeout"
        --output="$output"
        --ref_file="$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }"
        
    </command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" >
                <option value="text">Copy/paste your identifiers</option>
                <option value="file" selected="true">Input file containing IDs</option>
            </param>
            <when value="text" >
                <param name="txt" type="text" label="Copy/paste IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
                    <sanitizer invalid_char="">
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping initial="none">

                        </mapping>
                    </sanitizer>
                </param>
            </when>
            <when value="file" >
                <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
                <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
            </when>
        </conditional>
        <conditional name="species">
            <param name="mapping_file" type="select" label="Species" >
                <options from_data_table="proteore_id_mapping"/>
                <option value="human_id_mapping"></option>
                <option value="mouse_id_mapping"></option>
                <option value="rat_id_mapping"></option>
            </param>
            <when value="human_id_mapping">
                <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                    <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                    <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
                    <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                    <option value="GO" >GO terms (Gene Ontology) ID (e.g. GO:0070062)</option>
                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                    <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                </param>
                <section name="idto" title="Target type" expanded="True" >
                    <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
                        <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                        <option value="UniProt-AC" >UniProt accession number (e.g. P31946)</option>
                        <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                        <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                        <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                        <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                        <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="mouse_id_mapping">
                <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                    <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
                    <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                    <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                </param>
                <section name="idto" title="Target type of IDs" expanded="True" >
                    <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
                        <option value="UniProt-AC" >UniProt accession number (e.g. P31946)</option>
                        <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                        <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                        <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                        <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
            <when value="rat_id_mapping">
                <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
                    <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                    <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                    <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                    <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                    <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
                    <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                    <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                </param>
                <section name="idto" title="Target type of IDs" expanded="True" >
                    <param name="idtypeout" type="select" label="Target type of IDs you would like to map to" display="checkboxes" multiple="True" optional="false" >
                        <option value="UniProt-AC" >UniProt accession number (e.g. P31946)</option>
                        <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
                        <option value="GeneID" >Entrez gene ID (e.g. 7529)</option>
                        <option value="RefSeq" >RefSeq (NCBI) protein (e.g.  NP_003395.1)</option>
                        <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
                    </param>
                </section>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="tsv" />
    </outputs>
    <tests>
        <test>
            <conditional name="input" >
                <param name="ids" value="file"/>

                <param name="header" value="true" />
                <param name="ncol" value="c1"/>
            </conditional>
            <conditional name="species">
                <param name="mapping_file" value="human_id_mapping"/>
                <param name="idtypein" value="UniProt-AC"/>
                <section name="idto">
                    <param name="idtypeout" value="neXtProt,UniProt-ID,GeneID,MIM,Ensembl" />
                </section>
            </conditional>
            <output name="output" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
        </test>
    </tests>
    <help><![CDATA[
**Description**
This tool converts a list of identifiers (IDs) into another type of ID. Currently the conversion of IDs applies to the following three species: Human (homo sapiens, Mouse (Mus musculus), Rat (Rattus norvegicus). 
Supported source and target type of IDs are listed below. After choosing the type of your input IDs, you can select one or more types of ID you may need. 

-----

**Input**

A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing the mapped IDs. 
If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.

.. class:: warningmark

Accession numbers with an hyphen ("-") that normally correspond to isoform are considered as similar to its canonical form.
For example, "Q71U36-2" will be treated as "Q71U36".

-----

**Parameters**
Target type of IDs currently supported:   

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

* GI (NCBI GI number) (e.g. 21328448)

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

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

* Ensembl transcript ID (e.g. ENST00000353703)

* Ensembl protein ID (e.g. ENSP00000300161)

* BioGrid (e.g. 113361)

* STRING (e.g. 9606.ENSP00000300161)

* KEGG gene id (e.g. hsa:7529)

.. class:: warningmark 

Nextprot and OMIM only applicable to Human species.

-----

**Output**

A text file containing the selected type of IDs (in addition to the original column(s) provided)
Please, note that a "NA" is returned when there is no match between a source ID and the corresponding target ID.

-----

**Data sources (release date)**

This tool converts human IDs using the following source files:

- **HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
- **HUMAN_9606_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
- **nextprot_ac_list_all.txt (Nextprot released on 10/10/2018)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/
- **MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
- **MOUSE_10090_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
- **RAT_10116_idmapping.dat (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
- **RAT_10116_idmapping_selected.tab (Uniprot 23/10/18)**: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/

-----

.. class:: infomark

**Authors**

David Christiany, 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, 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.