Mercurial > repos > proteore > proteore_id_converter

diff id_converter.xml @ 29:1c5ee67c7836 draft

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planemo upload commit 03015f58ac7e7ba3cc44ba0d8899eacfaaf5a134-dirty
author proteore
date Thu, 09 May 2019 08:20:35 -0400
parents ba9eb6c631d6
children 8c36d6846f6f
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line diff
--- a/id_converter.xml	Thu May 09 05:42:19 2019 -0400
+++ b/id_converter.xml	Thu May 09 08:20:35 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="IDconverter" name="ID Converter" version="2019.05.09.5">
+<tool id="IDconverter" name="ID Converter" version="2019.05.09.6">
     <description>(Human, Mouse, Rat)
     </description>
     <requirements>
@@ -90,8 +90,8 @@
                 <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" >UniProt accession number (reviewed only)</option>
+                        <option value="UniProt-AC_reviewed" >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-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>
@@ -136,8 +136,8 @@
                 </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. P31946)</option>
-                        <option value="UniProt-AC_reviewed" >UniProt accession number (reviewed only)</option>
+                        <option value="UniProt-AC_reviewed" >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-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>
@@ -181,8 +181,8 @@
                 </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. P31946)</option>
-                        <option value="UniProt-AC_reviewed" >UniProt accession number (reviewed only)</option>
+                        <option value="UniProt-AC_reviewed" >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-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>
@@ -247,7 +247,9 @@
 
 * neXtProt ID (e.g. NX_P31946)
 
-* UniProt accession number (e.g. P31946)
+* UniProt accession number (e.g. P31946 - reviewed entries only)
+
+* UniProt accession number (e.g. P31946 - reviewed and unreviewed entries)
 
 * UniProt ID (e.g 1433B_HUMAN)
 
@@ -298,11 +300,14 @@
 
 - **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>`_.
 
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