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>`_.
 
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