Mercurial > repos > proteore > proteore_id_converter

diff id_converter.xml @ 46:2152ae70c6c9 draft

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"planemo upload commit d60b7f0387c28a474ce34923960458020aa2e29e-dirty"
author proteore
date Thu, 12 Dec 2019 10:46:53 +0000
parents 845b7cee353c
children e6b93b3b3a1c
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line diff
--- a/id_converter.xml	Thu Jun 27 04:19:21 2019 -0400
+++ b/id_converter.xml	Thu Dec 12 10:46:53 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="IDconverter" name="ID Converter" version="2019.06.27">
+<tool id="IDconverter" name="ID Converter" version="2019.12.12">
     <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>
@@ -91,9 +93,10 @@
                     <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_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>
@@ -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>
@@ -136,9 +141,10 @@
                 <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_reviewed" selected="True" >UniProt accession number - reviewed 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>
@@ -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>
@@ -180,9 +188,10 @@
                 <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_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>
@@ -283,13 +292,13 @@
 
 * KEGG gene id (e.g. hsa:7529)
 
-.. class:: warningmark 
-
-Nextprot and OMIM only applicable to Human species.
-
 .. 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 selection
+
+- **Nextprot** and **OMIM** only applicable to Human species.
+- **Uniprot-AC reviewed entries only**: only reviewed IDs are considered here
+- **Uniprot-AC**: All uniprot-AC are considered (reviewed and unreviewed entries).
 
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