Mercurial > repos > proteore > proteore_id_converter
diff id_converter.xml @ 19:9d758344d36e draft
planemo upload commit 339ab77a83db03409c8001324f10b36ff5b13a39-dirty
| author | proteore |
|---|---|
| date | Wed, 19 Jun 2019 04:38:12 -0400 |
| parents | 5252bbcfbdd7 |
| children | 77a2cd4162b7 |
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--- a/id_converter.xml Fri May 10 10:38:46 2019 -0400 +++ b/id_converter.xml Wed Jun 19 04:38:12 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="IDconverter" name="ID Converter" version="2019.05.10"> +<tool id="IDconverter" name="ID Converter" version="2019.06.18"> <description>(Human, Mouse, Rat) </description> <requirements> @@ -59,8 +59,8 @@ <conditional name="species"> <param name="species" type="select" label="Species"> <option value="Human" selected="True">Human (Homo sapiens)</option> - <option value="Mouse" selected="True">Mouse (Mus musculus)</option> - <option value="Rat" selected="True">Rat (Rattus norvegicus)</option> + <option value="Mouse">Mouse (Mus musculus)</option> + <option value="Rat">Rat (Rattus norvegicus)</option> </param> <when value="Human"> <param name="mapping_file" type="select" label="Release" > @@ -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> @@ -217,7 +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" /> @@ -238,7 +236,11 @@ .. class:: warningmark Accession numbers with an hyphen ("-") that normally correspond to isoform are considered as similar to its canonical form. -For example, "Q71U36-2" will be treated as "Q71U36". +For example, "Q71U36-2" will be treated as "Q71U36". + +.. class:: warningmark + +In copy/paste mode, the number of IDs considered in input is limited to 5000. ----- @@ -249,9 +251,7 @@ * 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) +* UniProt ID (e.g 1433B_HUMAN - reviewed entries only) * Entrez gene ID (e.g. 7529) @@ -285,6 +285,10 @@ Nextprot and OMIM only applicable to Human species. +.. class:: warningmark + +For Uniprot-AC and uniprot-ID, only reviewed IDs are considered here, except for releases before 08-05-2019 where all uniprot-AC and uniprot-ID (at the time) are considered. + ----- **Output** @@ -298,16 +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>`_. -----