Mercurial > repos > proteore > proteore_id_converter

diff id_converter.xml @ 34:eb1176711d9f draft

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planemo upload commit 5c2c274361c0daceae1f678eca0e6c0d5b4ba4f7-dirty
author proteore
date Mon, 27 May 2019 08:06:58 -0400
parents 6dfe5e809163
children bfd4421f56e9
line wrap: on
line diff
--- a/id_converter.xml	Thu May 16 11:14:23 2019 -0400
+++ b/id_converter.xml	Mon May 27 08:06:58 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="IDconverter" name="ID Converter" version="2019.05.16.1">
+<tool id="IDconverter" name="ID Converter" version="2019.05.27">
     <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_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-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-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>
@@ -117,41 +117,40 @@
                     </options>
                 </param>    
                 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
-                    <option value="UniProt-AC" selected="True" >UniProt accession number (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="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>
-                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
-                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
-                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
-                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
-                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
-                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
-                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
-                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
-                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
-                    <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
+                    <option value="UniProt-AC" selected="True" >UniProt accession number (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="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>
+                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0051607)</option>
+                    <option value="PIR" >Protein Information Resource ID (e.g. A93261)</option>
+                    <option value="UniGene" >Unigene ID (e.g. Mm.1293)</option>
+                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSMUSG00000031239)</option>
+                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENSMUST00000033591)</option>
+                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSMUSP00000033591)</option>
+                    <option value="BioGrid" >BioGrid (e.g. 201578)</option>
+                    <option value="STRING" >STRING (e.g. 10090.ENSMUSP00000041712)</option>
+                    <option value="KEGG" >KEGG gene id (e.g. mmu:217845)</option>
                 </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_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>
-                        <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
-                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
-                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
-                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
-                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
-                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
-                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
-                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
-                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
-                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
-                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
+                        <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-ID" >UniProt ID (e.g IF27B_MOUSE)</option>
+                        <option value="GeneID" >Entrez gene ID (e.g. 217845)</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>
+                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0051607)</option>
+                        <option value="PIR" >Protein Information Resource ID (e.g. A93261)</option>
+                        <option value="UniGene" >Unigene ID (e.g. Mm.1293)</option>
+                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSMUSG00000031239)</option>
+                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENSMUST00000033591)</option>
+                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSMUSP00000033591)</option>
+                        <option value="BioGrid" >BioGrid (e.g. 201578)</option>
+                        <option value="STRING" >STRING (e.g. 10090.ENSMUSP00000041712)</option>
+                        <option value="KEGG" >KEGG gene id (e.g. mmu:217845)</option>
                     </param>
                 </section>
             </when>
@@ -162,41 +161,40 @@
                     </options>
                 </param>    
                 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
-                    <option value="UniProt-AC" selected="True" >UniProt accession number (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="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>
-                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
-                    <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
-                    <option value="MIM" >OMIM (Online Mendelian Inheritance in Man database) ID (e.g: 601289)</option>
-                    <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
-                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
-                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
-                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
-                    <option value="BioGrid" >BioGrid (e.g. 113361)</option>
-                    <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
-                    <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
+                    <option value="UniProt-AC" >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="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>
+                    <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0005737)</option>
+                    <option value="PIR" >Protein Information Resource ID (e.g. PT0204)</option>
+                    <option value="UniGene" >Unigene ID (e.g. Rn.34914)</option>
+                    <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSRNOG00000019047)</option>
+                    <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENSRNOT00000026040)</option>
+                    <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSRNOP00000026040)</option>
+                    <option value="BioGrid" >BioGrid (e.g. 253944)</option>
+                    <option value="STRING" >STRING (e.g. 10116.ENSRNOP00000054039)</option>
+                    <option value="KEGG" >KEGG gene id (e.g. rno:296488)</option>
                 </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_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>
-                        <option value="GI" >GI (NCBI GI number) (e.g. 21328448)</option>
-                        <option value="PDB" >Protein DataBank ID (e.g. 2BR9:A)</option>
-                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0070062)</option>
-                        <option value="PIR" >Protein Information Resource ID (e.g. S34755)</option>
-                        <option value="UniGene" >Unigene ID (e.g. Hs.643544)</option>
-                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSG00000166913)</option>
-                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENST00000353703)</option>
-                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSP00000300161)</option>
-                        <option value="BioGrid" >BioGrid (e.g. 113361)</option>
-                        <option value="STRING" >STRING (e.g. 9606.ENSP00000300161)</option>
-                        <option value="KEGG" >KEGG gene id (e.g. hsa:7529)</option>
+                        <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-ID" >UniProt ID (e.g OLA1_RAT)</option>
+                        <option value="GeneID" >Entrez gene ID (e.g. 296488)</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>
+                        <option value="GO" >GOterms (Gene Ontology) ID (e.g. GO:0005737)</option>
+                        <option value="PIR" >Protein Information Resource ID (e.g. PT0204)</option>
+                        <option value="UniGene" >Unigene ID (e.g. Rn.34914)</option>
+                        <option value="Ensembl_Gene" >Ensembl gene ID (e.g. ENSRNOG00000019047)</option>
+                        <option value="Ensembl_Transcript" >Ensembl transcript ID (e.g. ENSRNOT00000026040)</option>
+                        <option value="Ensembl_Protein" >Ensembl protein ID (e.g. ENSRNOP00000026040)</option>
+                        <option value="BioGrid" >BioGrid (e.g. 253944)</option>
+                        <option value="STRING" >STRING (e.g. 10116.ENSRNOP00000054039)</option>
+                        <option value="KEGG" >KEGG gene id (e.g. rno:296488)</option>
                     </param>
                 </section>
             </when>