| 1 | <tool id="hgv_ctdBatch" name="CTD" version="1.0.0"> |
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| 2 | <description>analysis of chemicals, diseases, or genes</description> |
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| 3 | |
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| 4 | <command interpreter="perl"> |
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| 5 | ctd.pl $input $numerical_column $inType.inputType |
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| 6 | #if $inType.inputType == "disease" |
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| 7 | $inType.report ANY |
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| 8 | #else if $inType.reportType.report == "cgixns" |
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| 9 | $inType.reportType.report $inType.reportType.actType |
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| 10 | #else |
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| 11 | $inType.reportType.report ANY |
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| 12 | #end if |
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| 13 | $out_file1 |
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| 14 | </command> |
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| 15 | |
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| 16 | <inputs> |
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| 17 | <param name="input" type="data" format="tabular" label="Dataset" /> |
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| 18 | <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" /> |
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| 19 | <conditional name="inType"> |
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| 20 | <param name="inputType" label="Identifier type" type="select"> |
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| 21 | <option value="chem">Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs)</option> |
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| 22 | <option value="disease">Diseases (MeSH or OMIM names, synonyms or accession IDs)</option> |
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| 23 | <option value="gene" selected="true">Genes (NCBI official symbols or accession IDs)</option> |
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| 24 | </param> |
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| 25 | <when value="chem"> |
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| 26 | <conditional name='reportType'> |
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| 27 | <param name="report" label="Data to extract" type="select"> |
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| 28 | <option value="cgixns">Curated chemical-gene interactions</option> |
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| 29 | <option value="genes">Curated gene associations</option> |
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| 30 | <option value="pathways">Pathway associations</option> |
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| 31 | <option value="diseases" selected="true">All disease relationships</option> |
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| 32 | <option value="diseases_direct"> Direct disease relationships only</option> |
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| 33 | <option value="diseases_inferred"> Inferred disease relationships only</option> |
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| 34 | <option value="go">All GO associations</option> |
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| 35 | <option value="go_p"> GO biological Processes only</option> |
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| 36 | <option value="go_f"> GO molecular Functions only</option> |
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| 37 | <option value="go_c"> GO cellular Components only</option> |
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| 38 | </param> |
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| 39 | <when value="genes"> |
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| 40 | <!-- do nothing --> |
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| 41 | </when> |
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| 42 | <when value="pathways"> |
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| 43 | <!-- do nothing --> |
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| 44 | </when> |
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| 45 | <when value="diseases"> |
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| 46 | <!-- do nothing --> |
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| 47 | </when> |
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| 48 | <when value="diseases_direct"> |
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| 49 | <!-- do nothing --> |
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| 50 | </when> |
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| 51 | <when value="diseases_inferred"> |
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| 52 | <!-- do nothing --> |
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| 53 | </when> |
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| 54 | <when value="go"> |
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| 55 | <!-- do nothing --> |
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| 56 | </when> |
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| 57 | <when value="go_p"> |
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| 58 | <!-- do nothing --> |
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| 59 | </when> |
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| 60 | <when value="go_f"> |
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| 61 | <!-- do nothing --> |
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| 62 | </when> |
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| 63 | <when value="go_c"> |
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| 64 | <!-- do nothing --> |
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| 65 | </when> |
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| 66 | <when value="cgixns"> |
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| 67 | <param name="actType" label="Interaction type" type="select"> |
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| 68 | <option value="ANY">ANY</option> |
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| 69 | <option value="abundance">abundance</option> |
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| 70 | <option value="activity">activity</option> |
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| 71 | <option value="binding">binding</option> |
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| 72 | <option value="cotreatment">cotreatment</option> |
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| 73 | <option value="expression">expression</option> |
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| 74 | <option value="folding">folding</option> |
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| 75 | <option value="localization">localization</option> |
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| 76 | <option value="metabolic processing">metabolic processing</option> |
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| 77 | <option value="acetylation">- acetylation</option> |
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| 78 | <option value="acylation">- acylation</option> |
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| 79 | <option value="alkylation">- alkylation</option> |
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| 80 | <option value="amination">- amination</option> |
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| 81 | <option value="carbamoylation">- carbamoylation</option> |
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| 82 | <option value="carboxylation">- carboxylation</option> |
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| 83 | <option value="chemical synthesis">- chemical synthesis</option> |
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| 84 | <option value="degradation">- degradation</option> |
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| 85 | <option value="cleavage"> - cleavage</option> |
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| 86 | <option value="hydrolysis"> - hydrolysis</option> |
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| 87 | <option value="ethylation">- ethylation</option> |
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| 88 | <option value="glutathionylation">- glutathionylation</option> |
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| 89 | <option value="glycation">- glycation</option> |
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| 90 | <option value="glycosylation">- glycosylation</option> |
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| 91 | <option value="N-linked glycosylation"> - N-linked glycosylation</option> |
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| 92 | <option value="O-linked glycosylation"> - O-linked glycosylation</option> |
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| 93 | <option value="glucuronidation"> - glucuronidation</option> |
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| 94 | <option value="hydroxylation">- hydroxylation</option> |
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| 95 | <option value="lipidation">- lipidation</option> |
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| 96 | <option value="farnesylation"> - farnesylation</option> |
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| 97 | <option value="geranolyation"> - geranolyation</option> |
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| 98 | <option value="myristolylation"> - myristolylation</option> |
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| 99 | <option value="palmitoylation"> - palmitoylation</option> |
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| 100 | <option value="prenylation"> - prenylation</option> |
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| 101 | <option value="methylation">- methylation</option> |
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| 102 | <option value="nitrosation">- nitrosation</option> |
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| 103 | <option value="nucleotidylation">- nucleotidylation</option> |
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| 104 | <option value="oxidation">- oxidation</option> |
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| 105 | <option value="phosphorylation">- phosphorylation</option> |
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| 106 | <option value="reduction">- reduction</option> |
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| 107 | <option value="ribosylation">- ribosylation</option> |
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| 108 | <option value="ADP-ribosylation"> - ADP-ribosylation</option> |
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| 109 | <option value="sulfation">- sulfation</option> |
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| 110 | <option value="sumoylation">- sumoylation</option> |
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| 111 | <option value="ubiquitination">- ubiquitination</option> |
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| 112 | <option value="mutagenesis">mutagenesis</option> |
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| 113 | <option value="reaction">reaction</option> |
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| 114 | <option value="response to chemical">response to chemical</option> |
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| 115 | <option value="splicing">splicing</option> |
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| 116 | <option value="stability">stability</option> |
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| 117 | <option value="transport">transport</option> |
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| 118 | <option value="secretion">- secretion</option> |
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| 119 | <option value="export"> - export</option> |
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| 120 | <option value="uptake">- uptake</option> |
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| 121 | <option value="import"> - import</option> |
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| 122 | </param> |
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| 123 | </when> |
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| 124 | </conditional> |
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| 125 | </when> |
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| 126 | <when value="disease"> |
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| 127 | <param name="report" label="Data to extract" type="select"> |
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| 128 | <option value="chems">Chemical associations</option> |
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| 129 | <option value="chems_direct">Chemical associations direct relationships only</option> |
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| 130 | <option value="chems_inferred">Chemical associations inferred relationships only</option> |
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| 131 | <option value="genes">Curated gene associations</option> |
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| 132 | <option value="pathways">Pathway associations</option> |
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| 133 | </param> |
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| 134 | </when> |
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| 135 | <when value="gene"> |
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| 136 | <conditional name='reportType'> |
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| 137 | <param name="report" label="Data to extract" type="select"> |
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| 138 | <option value="cgixns">Curated chemical-gene interactions</option> |
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| 139 | <option value="chems">Curated chemical associations</option> |
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| 140 | <option value="pathways">Pathway associations</option> |
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| 141 | <option value="diseases" selected="true">All disease relationships</option> |
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| 142 | <option value="diseases_direct"> Direct disease relationships only</option> |
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| 143 | <option value="diseases_inferred"> Inferred disease relationships only</option> |
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| 144 | <option value="go">All GO associations</option> |
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| 145 | <option value="go_p"> GO biological Processes only</option> |
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| 146 | <option value="go_f"> GO molecular Functions only</option> |
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| 147 | <option value="go_c"> GO cellular Components only</option> |
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| 148 | </param> |
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| 149 | <when value="chems"> |
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| 150 | <!-- do nothing --> |
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| 151 | </when> |
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| 152 | <when value="pathways"> |
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| 153 | <!-- do nothing --> |
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| 154 | </when> |
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| 155 | <when value="diseases"> |
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| 156 | <!-- do nothing --> |
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| 157 | </when> |
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| 158 | <when value="diseases_direct"> |
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| 159 | <!-- do nothing --> |
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| 160 | </when> |
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| 161 | <when value="diseases_inferred"> |
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| 162 | <!-- do nothing --> |
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| 163 | </when> |
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| 164 | <when value="go"> |
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| 165 | <!-- do nothing --> |
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| 166 | </when> |
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| 167 | <when value="go_p"> |
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| 168 | <!-- do nothing --> |
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| 169 | </when> |
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| 170 | <when value="go_f"> |
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| 171 | <!-- do nothing --> |
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| 172 | </when> |
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| 173 | <when value="go_c"> |
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| 174 | <!-- do nothing --> |
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| 175 | </when> |
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| 176 | <when value="cgixns"> |
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| 177 | <param name="actType" label="Interaction type" type="select"> |
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| 178 | <option value="ANY">ANY</option> |
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| 179 | <option value="abundance">abundance</option> |
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| 180 | <option value="activity">activity</option> |
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| 181 | <option value="binding">binding</option> |
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| 182 | <option value="cotreatment">cotreatment</option> |
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| 183 | <option value="expression">expression</option> |
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| 184 | <option value="folding">folding</option> |
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| 185 | <option value="localization">localization</option> |
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| 186 | <option value="metabolic processing">metabolic processing</option> |
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| 187 | <option value="acetylation">- acetylation</option> |
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| 188 | <option value="acylation">- acylation</option> |
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| 189 | <option value="alkylation">- alkylation</option> |
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| 190 | <option value="amination">- amination</option> |
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| 191 | <option value="carbamoylation">- carbamoylation</option> |
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| 192 | <option value="carboxylation">- carboxylation</option> |
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| 193 | <option value="chemical synthesis">- chemical synthesis</option> |
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| 194 | <option value="degradation">- degradation</option> |
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| 195 | <option value="cleavage"> - cleavage</option> |
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| 196 | <option value="hydrolysis"> - hydrolysis</option> |
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| 197 | <option value="ethylation">- ethylation</option> |
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| 198 | <option value="glutathionylation">- glutathionylation</option> |
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| 199 | <option value="glycation">- glycation</option> |
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| 200 | <option value="glycosylation">- glycosylation</option> |
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| 201 | <option value="N-linked glycosylation"> - N-linked glycosylation</option> |
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| 202 | <option value="O-linked glycosylation"> - O-linked glycosylation</option> |
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| 203 | <option value="glucuronidation"> - glucuronidation</option> |
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| 204 | <option value="hydroxylation">- hydroxylation</option> |
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| 205 | <option value="lipidation">- lipidation</option> |
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| 206 | <option value="farnesylation"> - farnesylation</option> |
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| 207 | <option value="geranolyation"> - geranolyation</option> |
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| 208 | <option value="myristolylation"> - myristolylation</option> |
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| 209 | <option value="palmitoylation"> - palmitoylation</option> |
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| 210 | <option value="prenylation"> - prenylation</option> |
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| 211 | <option value="methylation">- methylation</option> |
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| 212 | <option value="nitrosation">- nitrosation</option> |
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| 213 | <option value="nucleotidylation">- nucleotidylation</option> |
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| 214 | <option value="oxidation">- oxidation</option> |
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| 215 | <option value="phosphorylation">- phosphorylation</option> |
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| 216 | <option value="reduction">- reduction</option> |
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| 217 | <option value="ribosylation">- ribosylation</option> |
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| 218 | <option value="ADP-ribosylation"> - ADP-ribosylation</option> |
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| 219 | <option value="sulfation">- sulfation</option> |
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| 220 | <option value="sumoylation">- sumoylation</option> |
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| 221 | <option value="ubiquitination">- ubiquitination</option> |
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| 222 | <option value="mutagenesis">mutagenesis</option> |
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| 223 | <option value="reaction">reaction</option> |
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| 224 | <option value="response to chemical">response to chemical</option> |
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| 225 | <option value="splicing">splicing</option> |
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| 226 | <option value="stability">stability</option> |
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| 227 | <option value="transport">transport</option> |
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| 228 | <option value="secretion">- secretion</option> |
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| 229 | <option value="export"> - export</option> |
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| 230 | <option value="uptake">- uptake</option> |
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| 231 | <option value="import"> - import</option> |
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| 232 | </param> |
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| 233 | </when> |
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| 234 | </conditional> |
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| 235 | </when> |
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| 236 | </conditional> |
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| 237 | </inputs> |
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| 238 | |
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| 239 | <outputs> |
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| 240 | <data format="tabular" name="out_file1" /> |
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| 241 | </outputs> |
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| 242 | |
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| 243 | <!-- broken for now. will be fixed soon. |
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| 244 | <tests> |
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| 245 | <test> |
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| 246 | <param name="input" ftype="tabular" value="ctdBatchInput.txt" /> |
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| 247 | <param name="numerical_column" value="1" /> |
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| 248 | <param name="inputType" value="gene" /> |
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| 249 | <param name="report" value="diseases" /> |
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| 250 | <output name="out_file1" file="ctdBatchOut.txt" /> |
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| 251 | </test> |
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| 252 | </tests> |
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| 253 | --> |
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| 254 | |
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| 255 | <help> |
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| 256 | **Dataset formats** |
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| 257 | |
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| 258 | The input and output datasets are tabular_. |
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| 259 | (`Dataset missing?`_) |
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| 260 | |
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| 261 | .. _tabular: ./static/formatHelp.html#tab |
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| 262 | .. _Dataset missing?: ./static/formatHelp.html |
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| 263 | |
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| 264 | ----- |
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| 265 | |
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| 266 | **What it does** |
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| 267 | |
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| 268 | This tool extracts data related to the provided list of identifiers |
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| 269 | from the Comparative Toxicogenomics Database (CTD). The fields |
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| 270 | extracted vary with the type of data requested; the first row |
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| 271 | of the output identifies the columns. |
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| 272 | |
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| 273 | For the curated chemical-gene interactions, you can also choose the |
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| 274 | interaction type from the search-and-select box. The choices that |
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| 275 | start with '-' are a subset of a choice above them; you can chose |
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| 276 | either the general interaction type or a more specific one. |
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| 277 | |
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| 278 | Website: http://ctd.mdibl.org/ |
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| 279 | |
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| 280 | ----- |
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| 281 | |
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| 282 | **Examples** |
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| 283 | |
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| 284 | - input data file: |
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| 285 | HBB |
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| 286 | |
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| 287 | - select Column = c1, Identifier type = Genes, and Data to extract = All disease relationships |
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| 288 | |
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| 289 | - output file:: |
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| 290 | |
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| 291 | #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs |
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| 292 | hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900 |
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| 293 | hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741 |
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| 294 | etc. |
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| 295 | |
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| 296 | Another example: |
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| 297 | |
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| 298 | - same input file: |
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| 299 | HBB |
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| 300 | |
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| 301 | - select Column = c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY |
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| 302 | |
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| 303 | - output file:: |
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| 304 | |
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| 305 | #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs |
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| 306 | hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347 |
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| 307 | hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499 |
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| 308 | etc. |
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| 309 | |
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| 310 | ----- |
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| 311 | |
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| 312 | **Reference** |
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| 313 | |
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| 314 | Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009) |
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| 315 | Comparative Toxicogenomics Database: a knowledgebase and discovery tool for |
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| 316 | chemical-gene-disease networks. |
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| 317 | Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9. |
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| 318 | |
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| 319 | </help> |
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| 320 | </tool> |
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