Mercurial > repos > proteore > proteore_id_converter
diff id_converter.xml @ 18:5252bbcfbdd7 draft
planemo upload commit dc6d9d8f1808c4c6bcc42ac6861a8b811e4cee58-dirty
| author | proteore |
|---|---|
| date | Fri, 10 May 2019 10:38:46 -0400 |
| parents | 1e45ea50f145 |
| children | 9d758344d36e |
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--- a/id_converter.xml Thu Mar 07 07:49:18 2019 -0500 +++ b/id_converter.xml Fri May 10 10:38:46 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="IDconverter" name="ID Converter" version="2019.03.07"> +<tool id="IDconverter" name="ID Converter" version="2019.05.10"> <description>(Human, Mouse, Rat) </description> <requirements> @@ -64,7 +64,9 @@ </param> <when value="Human"> <param name="mapping_file" type="select" label="Release" > - <options from_data_table="proteore_id_mapping_Human"/> + <options from_data_table="proteore_id_mapping_Human"> + <filter type="sort_by" column="0"/> + </options> </param> <param name="idtypein" type="select" label="Type/source of IDs" optional="false" > <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> @@ -88,7 +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 (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> @@ -109,7 +112,9 @@ </when> <when value="Mouse"> <param name="mapping_file" type="select" label="Release" > - <options from_data_table="proteore_id_mapping_Mouse"/> + <options from_data_table="proteore_id_mapping_Mouse"> + <filter type="sort_by" column="0"/> + </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> @@ -131,7 +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 (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> @@ -151,7 +157,9 @@ </when> <when value="Rat"> <param name="mapping_file" type="select" label="Release" > - <options from_data_table="proteore_id_mapping_Rat"/> + <options from_data_table="proteore_id_mapping_Rat"> + <filter type="sort_by" column="0"/> + </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> @@ -173,7 +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 (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> @@ -238,7 +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) @@ -289,11 +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>`_. -----