Mercurial > repos > proteore > proteore_id_converter
diff id_converter.xml @ 44:a6cac36db667 draft
planemo upload commit 527d0a74bb29e68317151d180407a691b50b0f61
| author | proteore |
|---|---|
| date | Tue, 18 Jun 2019 04:21:34 -0400 |
| parents | 878331083a00 |
| children | 845b7cee353c |
line wrap: on
line diff
--- a/id_converter.xml Fri Jun 14 09:48:31 2019 -0400 +++ b/id_converter.xml Tue Jun 18 04:21:34 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="IDconverter" name="ID Converter" version="2019.06.14.1"> +<tool id="IDconverter" name="ID Converter" version="2019.06.18"> <description>(Human, Mouse, Rat) </description> <requirements> @@ -215,7 +215,7 @@ <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" /> + <param name="idtypeout" value="neXtProt,UniProt-ID,GeneID,MIM,Ensembl_Gene" /> </section> </conditional> <output name="output" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" /> @@ -240,7 +240,7 @@ .. class:: warningmark -The number limit of IDs allowed in copy/paste is 5000. +In copy/paste mode, the number of IDs considered in input is limited to 5000. ----- @@ -302,16 +302,19 @@ 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/ -- `Human uniprot-AC entries reviewed <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606&format=list>`_. -- **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/ -- `Mouse uniprot-AC entries reviewed <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10090&format=list>`_. -- **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/ -- `Rat uniprot-AC entries reviewed <https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:10116&format=list>`_. +- 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>`_. -----
