Mercurial > repos > proteore > proteore_id_converter
diff id_converter.xml @ 21:6e65e1c78705 draft default tip
"planemo upload commit 540dd383c0617193db43bf11457011888751b022-dirty"
| author | proteore |
|---|---|
| date | Thu, 23 Jan 2020 08:43:51 -0500 |
| parents | 77a2cd4162b7 |
| children |
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--- a/id_converter.xml Fri Jun 28 05:12:40 2019 -0400 +++ b/id_converter.xml Thu Jan 23 08:43:51 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="IDconverter" name="ID Converter" version="2019.06.27"> +<tool id="IDconverter" name="ID Converter" version="2020.01.09"> <description>(Human, Mouse, Rat) </description> <requirements> @@ -71,8 +71,10 @@ <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-AC_reviewed" selected="True" >UniProt accession number - reviewed only (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="Gene_Name" >Gene Name (e.g. YWHAB)</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> @@ -90,10 +92,11 @@ <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 - reviewed entries only)</option> - <!--option value="UniProt-AC" >UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)</option--> + <option value="UniProt-AC" >UniProt accession number (e.g. P31946) - reviewed and unreviewed entries</option> + <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number (e.g. P31946) - reviewed entries only</option> <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option> <option value="GeneID" >Entrez gene ID (e.g. 7529)</option> + <option value="Gene_Name" >Gene Name (e.g. YWHAB)</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> @@ -118,8 +121,10 @@ </param> <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. Q8VC49)</option> + <!--option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed entries only (e.g. Q8VC49)</option--> <option value="UniProt-ID" >UniProt ID (e.g IF27B_MOUSE)</option> <option value="GeneID" >Entrez gene ID (e.g. 217845)</option> + <option value="Gene_Name" >Gene Name (e.g. Ifi27l2b)</option> <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_663424.1)</option> <option value="GI" >GI (NCBI GI number) (e.g. 148686879)</option> <option value="PDB" >Protein DataBank ID (e.g. 2BDU:A)</option> @@ -135,10 +140,11 @@ </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. Q8VC49 - reviewed entries only)</option> - <!--option value="UniProt-AC" >UniProt accession number (e.g. Q8VC49 - reviewed and unreviewed entries)</option--> + <option value="UniProt-AC" >UniProt accession number (e.g. Q8VC49) - reviewed and unreviewed entries</option> + <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number (e.g. Q8VC49) - reviewed entries only</option> <option value="UniProt-ID" >UniProt ID (e.g IF27B_MOUSE)</option> <option value="GeneID" >Entrez gene ID (e.g. 217845)</option> + <option value="Gene_Name" >Gene Name (e.g. Ifi27l2b)</option> <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_663424.1)</option> <option value="GI" >GI (NCBI GI number) (e.g. 148686879)</option> <option value="PDB" >Protein DataBank ID (e.g. 2BDU:A)</option> @@ -161,9 +167,11 @@ </options> </param> <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" > - <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7 - reviewed entries only)</option> + <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7)</option> + <!--option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed entries only (e.g. A0JPJ7</option--> <option value="UniProt-ID" >UniProt ID (e.g OLA1_RAT)</option> <option value="GeneID" >Entrez gene ID (e.g. 296488)</option> + <option value="Gene_Name" >Gene Name (e.g. Ola1)</option> <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_001029099.1)</option> <option value="GI" >GI (NCBI GI number) (e.g. 117558623)</option> <option value="PDB" >Protein DataBank ID (e.g. 6EPD:O)</option> @@ -179,10 +187,11 @@ </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. A0JPJ7 - reviewed entries only)</option> - <!--option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7 - reviewed and unreviewed entries)</option--> + <option value="UniProt-AC" >UniProt accession number (e.g. A0JPJ7) - reviewed and unreviewed entries</option> + <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number (e.g. A0JPJ7) - reviewed entries only</option> <option value="UniProt-ID" >UniProt ID (e.g OLA1_RAT)</option> <option value="GeneID" >Entrez gene ID (e.g. 296488)</option> + <option value="Gene_Name" >Gene Name (e.g. Ola1)</option> <option value="RefSeq" >RefSeq (NCBI) protein (e.g. NP_001029099.1)</option> <option value="GI" >GI (NCBI GI number) (e.g. 117558623)</option> <option value="PDB" >Protein DataBank ID (e.g. 6EPD:O)</option> @@ -283,13 +292,19 @@ * KEGG gene id (e.g. hsa:7529) -.. class:: warningmark +.. class:: warningmark + +Output selection -Nextprot and OMIM only applicable to Human species. +- **Nextprot** and **OMIM** only applicable to Human species. +- **Uniprot-AC reviewed and unreviewed entries**: All uniprot-AC are considered. +- **Uniprot-AC reviewed entries only**: only reviewed IDs are considered here .. class:: warningmark -For Uniprot-AC and uniprot-ID, only reviewed IDs are considered here, except for release before 08-05-2019 where all uniprot-AC and uniprot-ID (at the time) are considered. +| Output Ids type needs to be different from input Ids type in order to create a new column of converted ids. +| For example, if you choose Entrez Gene ID in input ids type and in output ids type, no result column will be created. +| For multiple convertion, only output ids type different from the input ids type will create a column. ----- @@ -306,17 +321,7 @@ - Current release of Uniprot, for idmapping_selected.tab and idmapping.dat for Human, Mouse and Rat: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism - All previous release of uniprot can be found here: ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/ -- **nextprot_ac_list_all.txt (Nextprot released on 13/02/2019 - current)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/ -- All previous release of **nextprot_ac_list_all.txt** can be foud here: ftp://ftp.nextprot.org/pub/previous_releases/ -- `Human uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020190605]&format=list>`_. -- `Mouse uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020190605]&format=list>`_. -- `Rat uniprot-AC entries reviewed (05/06/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020190605]&format=list>`_. -- `Human uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020190508]&format=list>`_. -- `Mouse uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020190508]&format=list>`_. -- `Rat uniprot-AC entries reviewed (08/05/2019) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020190508]&format=list>`_. -- `Human uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+created:[20120720%20TO%2020181010]&format=list>`_. -- `Mouse uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090+AND+created:[20120720%20TO%2020181010]&format=list>`_. -- `Rat uniprot-AC entries reviewed (10/10/2018) <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116+AND+created:[20120720%20TO%2020181010]&format=list>`_. +- **nextprot_ac_list_all.txt (Nextprot released on 22/08/2019 - current)**: ftp://ftp.nextprot.org/pub/current_release/ac_lists/ -----