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author devteam
date Wed, 25 Sep 2013 10:23:26 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctd.xml	Wed Sep 25 10:23:26 2013 -0400
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+<tool id="ctdBatch_1" name="CTD" version="1.0.0">
+  <description>analysis of chemicals, diseases, or genes</description>
+  <command interpreter="perl">#if $inType.inputType=="disease" #ctd.pl $input $numerical_column $inType.inputType $inType.report ANY $out_file1
+#else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report "$inType.reportType.actType" $out_file1
+#else #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report ANY $out_file1
+#end if</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_inferred">Inferred pathway associations</option>
+	  <option value="pathways_enriched">Enriched pathway associations</option>
+          <option value="diseases" selected="true">All disease relationships</option>
+          <option value="diseases_curated">  Curated disease relationships only</option>
+          <option value="diseases_inferred">  Inferred disease relationships only</option>
+          <option value="go">All GO associations</option>
+          <option value="go_enriched">Enriched GO associations only</option>
+       </param>
+       <when value="genes">
+          <!-- do nothing -->
+       </when>
+       <when value="pathways_inferred">
+          <!-- do nothing -->
+       </when>
+       <when value="pathways_enriched">
+          <!-- do nothing -->
+       </when>
+       <when value="diseases">
+          <!-- do nothing -->
+       </when>
+       <when value="diseases_curated">
+          <!-- do nothing -->
+       </when>
+       <when value="diseases_inferred">
+          <!-- do nothing -->
+       </when>
+       <when value="go">
+          <!-- do nothing -->
+       </when>
+       <when value="go_enriched">
+          <!-- 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_curated">Curated chemical associations only</option>
+          <option value="chems_inferred">Inferred chemical associations only</option>
+          <option value="genes">Gene associations</option>
+          <option value="genes_curated">Curated gene associations</option>
+          <option value="genes_inferred">Inferred gene associations</option>
+          <option value="pathways_inferred">Inferred 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">Curated chemical associations</option>
+          <option value="pathways_curated">Curated pathway associations</option>
+          <option value="diseases" selected="true">All disease relationships</option>
+          <option value="diseases_curated">  Curated disease relationships only</option>
+          <option value="diseases_inferred">  Inferred disease relationships only</option>
+          <option value="go">All GO associations</option>
+       </param>
+       <when value="chems_curated">
+          <!-- do nothing -->
+       </when>
+       <when value="pathways_curated">
+          <!-- do nothing -->
+       </when>
+       <when value="diseases">
+          <!-- do nothing -->
+       </when>
+       <when value="diseases_curated">
+          <!-- do nothing -->
+       </when>
+       <when value="diseases_inferred">
+          <!-- do nothing -->
+       </when>
+       <when value="go">
+          <!-- 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>
+  <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_.  
+
+-----
+
+**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.
+
+Home page: http://ctdbase.org
+
+.. _tabular: ${static_path}/formatHelp.html#tab
+
+-----
+
+**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. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical.gene.disease networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92.
+
+
+</help>
+</tool>