Mercurial > repos > lnguyen > id_converter
diff id_converter.xml @ 0:02c549457875 draft default tip
planemo upload
| author | lnguyen |
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| date | Fri, 15 Sep 2017 06:02:03 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/id_converter.xml Fri Sep 15 06:02:03 2017 -0400 @@ -0,0 +1,189 @@ +<tool id="IDconverter" name="ID Converter" version="0.1.0"> + <description>converts identifiers which are of a different type/source to another type of identifiers and create the identifier lists. + </description> + <requirements> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="Rscript"> + id_converter_UniProt.R + "$idti.idtypein" + #if $input.ids == "text" + "$input.txt" + "list" + #else + "$input.file,$input.ncol,$input.header" + "file" + #end if + "$idto.idtypeout" + "$output" + $__tool_directory__/ID_mapping_Uniprot_HomoSapiens_20170809.txt + $__tool_directory__/Nextprot_Uniprot_id_mapping_file.txt + + </command> + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="text">Copy/paste your identifiers</option> + <option value="file">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 spaces into the form field, for example: P31946 P62258' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param name="ncol" type="text" label="The 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' /> + </when> + </conditional> + <conditional name="idti" > + <param name="idtypein" type="select" label="Select type/source of identifier of your list" > + <option value="neXtProt_ID" >neXtProt ID</option> + <option value="UNIPROT_AC" >Uniprot accession number</option> + <option value="UNIPROT_ID" >Uniprot ID</option> + <option value="GeneID_EntrezGene" >Entrez gene ID</option> + <option value="RefSeq" >RefSeq (NCBI) protein</option> + <option value="GI_number" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI</option> + <option value="PDB" >Protein DataBank ID</option> + <option value="GO_ID" >GOterms (Gene Ontology) ID</option> + <option value="PIR" >Protein Information Resource ID</option> + <option value="OMIM" >OMIM (Online Mendelian Inheritance in Man database) ID</option> + <option value="UniGene" >Unigene ID</option> + <option value="Ensembl.ENSG" >Ensembl gene ID</option> + <option value="Ensembl.ENST" >Ensembl transcript ID</option> + <option value="Ensembl.ENSP" >Ensembl protein ID</option> + </param> + <when value="neXtProt_ID" > + </when> + <when value="UNIPROT_AC" > + </when> + <when value="UNIPROT_ID" > + </when> + <when value="GeneID_EntrezGene" > + </when> + <when value="RefSeq" > + </when> + <when value="GI_number" > + </when> + <when value="PDB" > + </when> + <when value="GO_ID" > + </when> + <when value="PIR" > + </when> + <when value="OMIM" > + </when> + <when value="UniGene" > + </when> + <when value="Ensembl.ENSG" > + </when> + <when value="Ensembl.ENST" > + </when> + <when value="Ensembl.ENSP" > + </when> + </conditional> + <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" > + <option value="neXtProt_ID" >neXtProt ID</option> + <option value="UNIPROT_AC" >Uniprot accession number</option> + <option value="UNIPROT_ID" >Uniprot ID</option> + <option value="GeneID_EntrezGene" >Entrez gene ID</option> + <option value="RefSeq" >RefSeq (NCBI) protein</option> + <option value="GI_number" >GI (NCBI GI number) ID assigned to each sequence record processed by NCBI</option> + <option value="PDB" >Protein DataBank ID</option> + <option value="GO_ID" >GOterms (Gene Ontology) ID</option> + <option value="PIR" >Protein Information Resource ID</option> + <option value="OMIM" >OMIM (Online Mendelian Inheritance in Man database) ID</option> + <option value="UniGene" >Unigene ID</option> + <option value="Ensembl.ENSG" >Ensembl gene ID</option> + <option value="Ensembl.ENST" >Ensembl transcript ID</option> + <option value="Ensembl.ENSP" >Ensembl protein ID</option> + </param> + </section> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <conditional name="input"> + <param name="ids" value="file" /> + <param name="file" value="UnipIDs.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + </conditional> + <conditional name="idti"> + <param name="idtypein" value="UNIPROT_AC" /> + </conditional> + <section name="idto"> + <param name="idtypeout" value="Ensembl.ENSP,Ensembl.ENSG,neXtProt_ID" /> + </section> + <output name="output" file="output.txt" /> + </test> + </tests> + <help><![CDATA[ +This tool converts a list of IDs to another identifier type, select the source and target type from the dropdown menus above (see below supported source and target types). + +After choosing the type of input IDs, you can choose one or more types of IDs you would like to map to. + +If your input is a list of IDs or a single-column file, the tool will return a file containing the mapped IDs. + +If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file. + +**Available databases** + +* neXtProt ID + +* Uniprot accession number + +* Uniprot ID + +* Entrez gene ID + +* RefSeq (NCBI) protein + +* GI (NCBI GI number) ID assigned to each sequence record processed by NCBI + +* Protein DataBank ID + +* GOterms (Gene Ontology) ID + +* Protein Information Resource ID + +* OMIM (Online Mendelian Inheritance in Man database) ID + +* Unigene ID + +* Ensembl gene ID + +* Ensembl transcript ID + +* Ensembl protein ID + +----- + +.. class:: infomark + +**Authors** + +T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + ]]></help> + <citations> + </citations> +</tool>