Mercurial > repos > proteore > proteore_id_converter
diff id_converter.xml @ 10:8ea75a21fe30 draft
planemo upload commit 3acfbc891ef187832d56423c9351371805adc821-dirty
| author | proteore |
|---|---|
| date | Mon, 12 Nov 2018 08:19:39 -0500 |
| parents | cf91623c09f5 |
| children | 492a51f306c0 |
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--- a/id_converter.xml Thu Oct 25 04:35:27 2018 -0400 +++ b/id_converter.xml Mon Nov 12 08:19:39 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="IDconverter" name="ID Converter" version="2018.10.12"> +<tool id="IDconverter" name="ID Converter" version="2018.11.12"> <description>(Human, Mouse, Rat) </description> <requirements> @@ -31,7 +31,7 @@ <option value="file" selected="true">Input file containing your identifiers</option> </param> <when value="text" > - <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' > + <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' > <sanitizer invalid_char=""> <valid initial="string.printable"> <remove value="'"/> @@ -62,8 +62,8 @@ <when value="human_id_mapping"> <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" > <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.ID" >Uniprot ID (e.g 1433B_HUMAN)</option> + <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) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option> @@ -82,8 +82,8 @@ <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" help="Please see example of IDs in help section" > <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option> - <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option> - <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option> + <option value="UniProt-AC" >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) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option> @@ -103,8 +103,8 @@ </when> <when value="mouse_id_mapping"> <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" > - <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="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) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option> @@ -122,8 +122,8 @@ </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" help="Please see example of IDs in help section" > - <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option> - <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option> + <option value="UniProt-AC" >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) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option> @@ -142,8 +142,8 @@ </when> <when value="rat_id_mapping"> <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" > - <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="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) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option> @@ -161,8 +161,8 @@ </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" help="Please see example of IDs in help section" > - <option value="UniProt.AC" >Uniprot accession number (e.g. P31946)</option> - <option value="UniProt.ID" >Uniprot ID (e.g 1433B_HUMAN)</option> + <option value="UniProt-AC" >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) ID assigned to each sequence record processed by NCBI (e.g. 21328448)</option> @@ -194,9 +194,9 @@ </conditional> <conditional name="species"> <param name="mapping_file" value="human_id_mapping"/> - <param name="idtypein" value="UniProt.AC"/> + <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" /> </section> </conditional> <output name="output" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" /> @@ -257,19 +257,25 @@ This tool converts human IDs using the following source files: -* HUMAN_9606_idmapping_selected.tab (Uniprot 02/07/2018) +* HUMAN_9606_idmapping_selected.tab (Uniprot 23/10/2018) Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ -* HUMAN_9606_idmapping.dat (Uniprot 02/07/18) +* HUMAN_9606_idmapping.dat (Uniprot 23/10/18) Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ -* nextprot_ac_list_all.txt (Nextprot released on 17/01/2018) +* nextprot_ac_list_all.txt (Nextprot released on 10/10/2018) Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/ -* MOUSE_10090_idmapping_selected.tab (Uniprot 02/07/2018) +* MOUSE_10090_idmapping_selected.tab (Uniprot 23/10/2018) Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ -* MOUSE_10090_idmapping.dat (Uniprot 02/07/18) +* MOUSE_10090_idmapping.dat (Uniprot 23/10/18) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* RAT_10116_idmapping.dat (Uniprot 23/10/18) + Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ + +* RAT_10116_idmapping_selected.tab (Uniprot 23/10/18) Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ -----