diff id_converter.xml @ 48:135ef5524bfc draft

"planemo upload commit d78a9195d250f3d873f3c4ab67d1fa3ae58926f5-dirty"
author proteore
date Thu, 09 Jan 2020 11:09:45 +0000
parents e6b93b3b3a1c
children ab8ea848cc00
line wrap: on
line diff
--- a/id_converter.xml	Fri Dec 20 10:50:52 2019 +0000
+++ b/id_converter.xml	Thu Jan 09 11:09:45 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="IDconverter" name="ID Converter" version="2019.12.20">
+<tool id="IDconverter" name="ID Converter" version="2020.01.09">
     <description>(Human, Mouse, Rat)
     </description>
     <requirements>
@@ -92,8 +92,8 @@
                 <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-AC_reviewed" selected="True" >UniProt accession number - reviewed only (e.g. P31946)</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>
@@ -140,8 +140,8 @@
                 </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)</option>
-                        <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed only (e.g. Q8VC49)</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>
@@ -187,8 +187,8 @@
                 </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)</option>
-                        <option value="UniProt-AC_reviewed" selected="True" >UniProt accession number - reviewed entries only (e.g. A0JPJ7</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>
@@ -297,8 +297,14 @@
 Output selection
 
 - **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
-- **Uniprot-AC**: All uniprot-AC are considered (reviewed and unreviewed entries).
+
+.. class:: warningmark
+
+| 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. 
 
 -----
 
@@ -315,17 +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/
 
 -----