Mercurial > repos > xuebing > sharplabtool
diff tools/human_genome_variation/ctd.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/human_genome_variation/ctd.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,320 @@ +<tool id="hgv_ctdBatch" name="CTD" version="1.0.0"> + <description>analysis of chemicals, diseases, or genes</description> + + <command interpreter="perl"> + ctd.pl $input $numerical_column $inType.inputType + #if $inType.inputType == "disease" + $inType.report ANY + #else if $inType.reportType.report == "cgixns" + $inType.reportType.report $inType.reportType.actType + #else + $inType.reportType.report ANY + #end if + $out_file1 + </command> + + <inputs> + <param name="input" type="data" format="tabular" label="Dataset" /> + <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" /> + <conditional name="inType"> + <param name="inputType" label="Identifier type" type="select"> + <option value="chem">Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs)</option> + <option value="disease">Diseases (MeSH or OMIM names, synonyms or accession IDs)</option> + <option value="gene" selected="true">Genes (NCBI official symbols or accession IDs)</option> + </param> + <when value="chem"> + <conditional name='reportType'> + <param name="report" label="Data to extract" type="select"> + <option value="cgixns">Curated chemical-gene interactions</option> + <option value="genes">Curated gene associations</option> + <option value="pathways">Pathway associations</option> + <option value="diseases" selected="true">All disease relationships</option> + <option value="diseases_direct"> Direct disease relationships only</option> + <option value="diseases_inferred"> Inferred disease relationships only</option> + <option value="go">All GO associations</option> + <option value="go_p"> GO biological Processes only</option> + <option value="go_f"> GO molecular Functions only</option> + <option value="go_c"> GO cellular Components only</option> + </param> + <when value="genes"> + <!-- do nothing --> + </when> + <when value="pathways"> + <!-- do nothing --> + </when> + <when value="diseases"> + <!-- do nothing --> + </when> + <when value="diseases_direct"> + <!-- do nothing --> + </when> + <when value="diseases_inferred"> + <!-- do nothing --> + </when> + <when value="go"> + <!-- do nothing --> + </when> + <when value="go_p"> + <!-- do nothing --> + </when> + <when value="go_f"> + <!-- do nothing --> + </when> + <when value="go_c"> + <!-- do nothing --> + </when> + <when value="cgixns"> + <param name="actType" label="Interaction type" type="select"> + <option value="ANY">ANY</option> + <option value="abundance">abundance</option> + <option value="activity">activity</option> + <option value="binding">binding</option> + <option value="cotreatment">cotreatment</option> + <option value="expression">expression</option> + <option value="folding">folding</option> + <option value="localization">localization</option> + <option value="metabolic processing">metabolic processing</option> + <option value="acetylation">- acetylation</option> + <option value="acylation">- acylation</option> + <option value="alkylation">- alkylation</option> + <option value="amination">- amination</option> + <option value="carbamoylation">- carbamoylation</option> + <option value="carboxylation">- carboxylation</option> + <option value="chemical synthesis">- chemical synthesis</option> + <option value="degradation">- degradation</option> + <option value="cleavage"> - cleavage</option> + <option value="hydrolysis"> - hydrolysis</option> + <option value="ethylation">- ethylation</option> + <option value="glutathionylation">- glutathionylation</option> + <option value="glycation">- glycation</option> + <option value="glycosylation">- glycosylation</option> + <option value="N-linked glycosylation"> - N-linked glycosylation</option> + <option value="O-linked glycosylation"> - O-linked glycosylation</option> + <option value="glucuronidation"> - glucuronidation</option> + <option value="hydroxylation">- hydroxylation</option> + <option value="lipidation">- lipidation</option> + <option value="farnesylation"> - farnesylation</option> + <option value="geranolyation"> - geranolyation</option> + <option value="myristolylation"> - myristolylation</option> + <option value="palmitoylation"> - palmitoylation</option> + <option value="prenylation"> - prenylation</option> + <option value="methylation">- methylation</option> + <option value="nitrosation">- nitrosation</option> + <option value="nucleotidylation">- nucleotidylation</option> + <option value="oxidation">- oxidation</option> + <option value="phosphorylation">- phosphorylation</option> + <option value="reduction">- reduction</option> + <option value="ribosylation">- ribosylation</option> + <option value="ADP-ribosylation"> - ADP-ribosylation</option> + <option value="sulfation">- sulfation</option> + <option value="sumoylation">- sumoylation</option> + <option value="ubiquitination">- ubiquitination</option> + <option value="mutagenesis">mutagenesis</option> + <option value="reaction">reaction</option> + <option value="response to chemical">response to chemical</option> + <option value="splicing">splicing</option> + <option value="stability">stability</option> + <option value="transport">transport</option> + <option value="secretion">- secretion</option> + <option value="export"> - export</option> + <option value="uptake">- uptake</option> + <option value="import"> - import</option> + </param> + </when> + </conditional> + </when> + <when value="disease"> + <param name="report" label="Data to extract" type="select"> + <option value="chems">Chemical associations</option> + <option value="chems_direct">Chemical associations direct relationships only</option> + <option value="chems_inferred">Chemical associations inferred relationships only</option> + <option value="genes">Curated gene associations</option> + <option value="pathways">Pathway associations</option> + </param> + </when> + <when value="gene"> + <conditional name='reportType'> + <param name="report" label="Data to extract" type="select"> + <option value="cgixns">Curated chemical-gene interactions</option> + <option value="chems">Curated chemical associations</option> + <option value="pathways">Pathway associations</option> + <option value="diseases" selected="true">All disease relationships</option> + <option value="diseases_direct"> Direct disease relationships only</option> + <option value="diseases_inferred"> Inferred disease relationships only</option> + <option value="go">All GO associations</option> + <option value="go_p"> GO biological Processes only</option> + <option value="go_f"> GO molecular Functions only</option> + <option value="go_c"> GO cellular Components only</option> + </param> + <when value="chems"> + <!-- do nothing --> + </when> + <when value="pathways"> + <!-- do nothing --> + </when> + <when value="diseases"> + <!-- do nothing --> + </when> + <when value="diseases_direct"> + <!-- do nothing --> + </when> + <when value="diseases_inferred"> + <!-- do nothing --> + </when> + <when value="go"> + <!-- do nothing --> + </when> + <when value="go_p"> + <!-- do nothing --> + </when> + <when value="go_f"> + <!-- do nothing --> + </when> + <when value="go_c"> + <!-- do nothing --> + </when> + <when value="cgixns"> + <param name="actType" label="Interaction type" type="select"> + <option value="ANY">ANY</option> + <option value="abundance">abundance</option> + <option value="activity">activity</option> + <option value="binding">binding</option> + <option value="cotreatment">cotreatment</option> + <option value="expression">expression</option> + <option value="folding">folding</option> + <option value="localization">localization</option> + <option value="metabolic processing">metabolic processing</option> + <option value="acetylation">- acetylation</option> + <option value="acylation">- acylation</option> + <option value="alkylation">- alkylation</option> + <option value="amination">- amination</option> + <option value="carbamoylation">- carbamoylation</option> + <option value="carboxylation">- carboxylation</option> + <option value="chemical synthesis">- chemical synthesis</option> + <option value="degradation">- degradation</option> + <option value="cleavage"> - cleavage</option> + <option value="hydrolysis"> - hydrolysis</option> + <option value="ethylation">- ethylation</option> + <option value="glutathionylation">- glutathionylation</option> + <option value="glycation">- glycation</option> + <option value="glycosylation">- glycosylation</option> + <option value="N-linked glycosylation"> - N-linked glycosylation</option> + <option value="O-linked glycosylation"> - O-linked glycosylation</option> + <option value="glucuronidation"> - glucuronidation</option> + <option value="hydroxylation">- hydroxylation</option> + <option value="lipidation">- lipidation</option> + <option value="farnesylation"> - farnesylation</option> + <option value="geranolyation"> - geranolyation</option> + <option value="myristolylation"> - myristolylation</option> + <option value="palmitoylation"> - palmitoylation</option> + <option value="prenylation"> - prenylation</option> + <option value="methylation">- methylation</option> + <option value="nitrosation">- nitrosation</option> + <option value="nucleotidylation">- nucleotidylation</option> + <option value="oxidation">- oxidation</option> + <option value="phosphorylation">- phosphorylation</option> + <option value="reduction">- reduction</option> + <option value="ribosylation">- ribosylation</option> + <option value="ADP-ribosylation"> - ADP-ribosylation</option> + <option value="sulfation">- sulfation</option> + <option value="sumoylation">- sumoylation</option> + <option value="ubiquitination">- ubiquitination</option> + <option value="mutagenesis">mutagenesis</option> + <option value="reaction">reaction</option> + <option value="response to chemical">response to chemical</option> + <option value="splicing">splicing</option> + <option value="stability">stability</option> + <option value="transport">transport</option> + <option value="secretion">- secretion</option> + <option value="export"> - export</option> + <option value="uptake">- uptake</option> + <option value="import"> - import</option> + </param> + </when> + </conditional> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + + <!-- broken for now. will be fixed soon. + <tests> + <test> + <param name="input" ftype="tabular" value="ctdBatchInput.txt" /> + <param name="numerical_column" value="1" /> + <param name="inputType" value="gene" /> + <param name="report" value="diseases" /> + <output name="out_file1" file="ctdBatchOut.txt" /> + </test> + </tests> + --> + + <help> +**Dataset formats** + +The input and output datasets are tabular_. +(`Dataset missing?`_) + +.. _tabular: ./static/formatHelp.html#tab +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This tool extracts data related to the provided list of identifiers +from the Comparative Toxicogenomics Database (CTD). The fields +extracted vary with the type of data requested; the first row +of the output identifies the columns. + +For the curated chemical-gene interactions, you can also choose the +interaction type from the search-and-select box. The choices that +start with '-' are a subset of a choice above them; you can chose +either the general interaction type or a more specific one. + +Website: http://ctd.mdibl.org/ + +----- + +**Examples** + +- input data file: + HBB + +- select Column = c1, Identifier type = Genes, and Data to extract = All disease relationships + +- output file:: + + #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs + hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900 + hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741 + etc. + +Another example: + +- same input file: + HBB + +- select Column = c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY + +- output file:: + + #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs + hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347 + hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499 + etc. + +----- + +**Reference** + +Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009) +Comparative Toxicogenomics Database: a knowledgebase and discovery tool for +chemical-gene-disease networks. +Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9. + + </help> +</tool>