Mercurial > repos > proteore > proteore_id_converter
changeset 17:1e45ea50f145 draft
planemo upload commit 640429adac783e2354f5caf12d7b6b81b8ddf54f-dirty
| author | proteore |
|---|---|
| date | Thu, 07 Mar 2019 07:49:18 -0500 |
| parents | b6607b7e683f |
| children | 5252bbcfbdd7 |
| files | id_converter.py id_converter.xml proteore_id_mapping_Human.loc.sample proteore_id_mapping_Mouse.loc.sample proteore_id_mapping_Rat.loc.sample tool-data/proteore_id_mapping.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 7 files changed, 45 insertions(+), 18 deletions(-) [+] |
line wrap: on
line diff
--- a/id_converter.py Mon Jan 28 11:08:47 2019 -0500 +++ b/id_converter.py Thu Mar 07 07:49:18 2019 -0500 @@ -44,6 +44,7 @@ for line in input_file : if line != [] and set(line) != {''}: line[nb_col] = re.sub(r"\s+","",line[nb_col]) + if line[nb_col] == "" : line[nb_col]='NA' if ";" in line[nb_col] : ids = line[nb_col].split(";") for id in ids : @@ -119,6 +120,7 @@ if args.input_type=="file" : args.column_number = nb_col_to_int(args.column_number) header = str2bool(args.header) + #Get ref file to build dictionary csv.field_size_limit(sys.maxsize) # to handle big files @@ -151,7 +153,7 @@ if args.input_type == "list" : ids = get_input_ids_from_string(args.input) elif args.input_type == "file" : - input_file, ids = get_input_ids_from_file(args.input,args.column_number,args.header) + input_file, ids = get_input_ids_from_file(args.input,args.column_number,header) #Mapping ids result_dict = map_to_dictionary(ids,ids_dictionary,args.id_type,target_ids)
--- a/id_converter.xml Mon Jan 28 11:08:47 2019 -0500 +++ b/id_converter.xml Thu Mar 07 07:49:18 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="IDconverter" name="ID Converter" version="2019.01.28"> +<tool id="IDconverter" name="ID Converter" version="2019.03.07"> <description>(Human, Mouse, Rat) </description> <requirements> @@ -20,8 +20,11 @@ #end if --target_ids="$species.idto.idtypeout" --output="$output" - --ref_file="$__tool_directory__/${ filter( lambda x: str( x[2] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }" - + #if "id_mapping" in str($species.mapping_file).split("/") + --ref_file="$species.mapping_file" + #else + --ref_file="$__tool_directory__/$species.mapping_file" + #end if ]]></command> <inputs> <conditional name="input" > @@ -48,17 +51,21 @@ <when value="file" > <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol" type="text" value="c1" label="Column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> <conditional name="species"> - <param name="mapping_file" type="select" label="Species" > - <options from_data_table="proteore_id_mapping"/> - <option value="Human"></option> - <option value="Mouse"></option> - <option value="Rat"></option> + <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> </param> <when value="Human"> + <param name="mapping_file" type="select" label="Release" > + <options from_data_table="proteore_id_mapping_Human"/> + </param> <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> @@ -101,6 +108,9 @@ </section> </when> <when value="Mouse"> + <param name="mapping_file" type="select" label="Release" > + <options from_data_table="proteore_id_mapping_Mouse"/> + </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> @@ -140,6 +150,9 @@ </section> </when> <when value="Rat"> + <param name="mapping_file" type="select" label="Release" > + <options from_data_table="proteore_id_mapping_Rat"/> + </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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_id_mapping_Human.loc.sample Thu Mar 07 07:49:18 2019 -0500 @@ -0,0 +1,3 @@ +#This file lists the locations of reference file for id_converter tool +#<id> <name> <species> <value> +human_id_mapping_23-10-2018 Human (homo sapiens 23/10/2018) Human tool-data/human_id_mapping_23-10-2018.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_id_mapping_Mouse.loc.sample Thu Mar 07 07:49:18 2019 -0500 @@ -0,0 +1,3 @@ +#This file lists the locations of reference file for id_converter tool +#<id> <name> <species> <value> +mouse_id_mapping_23-10-2018 Mouse (Mus musculus 23/10/2018) Mouse tool-data/mouse_id_mapping_23-10-2018.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteore_id_mapping_Rat.loc.sample Thu Mar 07 07:49:18 2019 -0500 @@ -0,0 +1,3 @@ +#This file lists the locations of reference file for id_converter tool +#<id> <name> <species> <value> +rat_id_mapping_23-10-2018 Rat (Rattus norvegicus 23/10/2018) Rat tool-data/rat_id_mapping_23-10-2018.tsv
--- a/tool-data/proteore_id_mapping.loc.sample Mon Jan 28 11:08:47 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#This file lists the locations of reference file for id_converter tool -#<id> <name> <value> <path> -human_id_mapping_23-10-2018 Human (homo sapiens) Human tool-data/human_id_mapping_23-10-2018.tsv -mouse_id_mapping_23-10-2018 Mouse (Mus musculus) Mouse tool-data/mouse_id_mapping_23-10-2018.tsv -rat_id_mapping_23-10-2018 Rat (Rattus norvegicus) Rat tool-data/rat_id_mapping_23-10-2018.tsv
--- a/tool_data_table_conf.xml.sample Mon Jan 28 11:08:47 2019 -0500 +++ b/tool_data_table_conf.xml.sample Thu Mar 07 07:49:18 2019 -0500 @@ -1,7 +1,15 @@ <tables> <!-- Location of ID Mapping files for id_converter--> - <table name="proteore_id_mapping" comment_char="#"> - <columns>id, name, value, path</columns> - <file path="tool-data/proteore_id_mapping.loc" /> + <table name="proteore_id_mapping_Human" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_id_mapping_Human.loc" /> + </table> + <table name="proteore_id_mapping_Mouse" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_id_mapping_Mouse.loc" /> + </table> + <table name="proteore_id_mapping_Rat" comment_char="#"> + <columns>id, name, species, value</columns> + <file path="tool-data/proteore_id_mapping_Rat.loc" /> </table> </tables> \ No newline at end of file