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date Fri, 09 Mar 2012 19:37:19 -0500
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<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>