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1 <tool id="glytools_kegg_link" name="GAP Cross-reference with KEGG databases " version="0.3.1">
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2 <description> searches KEGG for related database entries</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
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5 </requirements>
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6 <command interpreter="python"><![CDATA[linkKEGG.py -t $targetdb -s $source -o $output ]]></command>
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7 <inputs>
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8 <param name="targetdb" type="select" label="Target Database">
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9 <option value="glycan" selected="true"> target KEGG glycan database</option>
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10 <option value="pathway" selected="false"> target KEGG pathway database</option>
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11 <option value="brite" selected="false"> target KEGG brite database</option>
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12 <option value="module" selected="false"> target KEGG module database</option>
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13 <option value="ko" selected="false"> target KEGG ko database</option>
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14 <option value="genome" selected="false"> target KEGG genome database</option>
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15 <option value="compound" selected="false"> target KEGG compound database</option>
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16 <option value="reaction" selected="false"> target KEGG reaction database</option>
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17 <option value="rpair" selected="false"> target KEGG rpair database</option>
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18 <option value="rclass" selected="false"> target KEGG rclass database</option>
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19 <option value="enzyme" selected="false"> target KEGG enzyme database</option>
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20 <option value="disease" selected="false"> target KEGG disease database</option>
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21 <option value="drug" selected="false"> target KEGG drug database</option>
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22 <option value="dgroup" selected="false"> target KEGG dgroup database</option>
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23 <option value="environ" selected="false"> target KEGG environ database</option>
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24 </param>
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25 <param name="source" type="text" value="ec:2.4.1.11" optional="false" label="Source database or entry" help="Source database or db entry to use to search target db. Example dbsource is genome. Example db entry is map00010"/>
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26 </inputs>
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27 <outputs>
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28 <data format="txt" name="output" label="linked entries from KEGG database search"/>
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29 </outputs>
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30 <citations>
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31 <!-- -->
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32 <citation type="doi">10.1002/0471250953.bi0112s38</citation>
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33 </citations>
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34 <tests>
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35 <test>
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36 <param name="targetdb" value="glycan" />
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37 <param name="source" value="ec:2.4.1.11"" />
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38 <output name="output" file="link_test1.txt" />
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39 </test>
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40 </tests>
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41 <help> <![CDATA[
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42 .. class:: infomark
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43
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44 **What this tool does**
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45
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46 This tool find connections between entries or db's found at KEGG. For instance which enzymes work on UDP-Glucose, or which reactions is UDP-Glucose involved in,
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47 or which glycans are acted by an enzyme that acts on UDP-Glucose (ec:2.4.1.11).
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48
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49 ----
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50
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51 .. class:: infomark
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52
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53 **Example 1**
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54
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55 target and source sequence::
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56
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57 enzyme
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58 gl:G10608
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59
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60 output sequence::
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61
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62 gl:G10608 ec:2.4.1.11
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63 gl:G10608 ec:2.4.1.12
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64 gl:G10608 ec:2.4.1.13
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65 gl:G10608 ec:2.4.1.14
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66 gl:G10608 ec:2.4.1.15
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67 gl:G10608 ec:2.4.1.183
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68 gl:G10608 ec:2.4.1.188
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69 gl:G10608 ec:2.4.1.34
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70 gl:G10608 ec:2.4.1.53
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71 gl:G10608 ec:2.4.1.80
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72
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73 .. class:: infomark
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74
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75 **Example 2**
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76
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77 target and source sequence::
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78
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79 reaction
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80 gl:G10608
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81
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82 output sequence::
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83
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84 gl:G10608 rn:R06020
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85 gl:G10608 rn:R06023
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86 gl:G10608 rn:R06036
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87 gl:G10608 rn:R06043
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88 gl:G10608 rn:R06045
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89 gl:G10608 rn:R06051
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90 gl:G10608 rn:R06062
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91 gl:G10608 rn:R06073
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92 gl:G10608 rn:R06181
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93 gl:G10608 rn:R06226
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94 gl:G10608 rn:R06275
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95 gl:G10608 rn:R09315
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96 gl:G10608 rn:R09316
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97
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98 .. class:: infomark
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99
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100 **Example 3**
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101
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102 target and source sequence::
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103
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104 glycan
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105 ec:2.4.1.11
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106
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107 output sequence::
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108
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109 ec:2.4.1.11 gl:G10495
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110 ec:2.4.1.11 gl:G10608
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111 ec:2.4.1.11 gl:G10619
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112
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113 ]]>
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114
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115 </help>
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116
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117 </tool>
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