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1 <tool id="glytools_kegg_find" name="GAP Find KEGG glycans " version="0.4.0">
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2 <description> using the KEGG database</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[ findKEGG.py -d $dbname -q $searchpattern -o $output ]]></command>
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7 <inputs>
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8 <param name="dbname" type="select" label="Database">
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9 <option value="glycan" selected="true"> search KEGG glycan database</option>
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10 <option value="pathway" selected="false"> search KEGG pathway database</option>
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11 <option value="brite" selected="false"> search KEGG brite database</option>
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12 <option value="module" selected="false"> search KEGG module database</option>
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13 <option value="ko" selected="false"> search KEGG ko database</option>
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14 <option value="genome" selected="false"> search KEGG genome database</option>
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15 <option value="compound" selected="false"> search KEGG compound database</option>
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16 <option value="reaction" selected="false"> search KEGG reaction database</option>
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17 <option value="rpair" selected="false"> search KEGG rpair database</option>
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18 <option value="rclass" selected="false"> search KEGG rclass database</option>
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19 <option value="enzyme" selected="false"> search KEGG enzyme database</option>
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20 <option value="disease" selected="false"> search KEGG disease database</option>
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21 <option value="drug" selected="false"> search KEGG drug database</option>
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22 <option value="dgroup" selected="false"> search KEGG dgroup database</option>
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23 <option value="environ" selected="false"> search KEGG environ database</option>
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24 </param>
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25 <param name="searchpattern" type="text" value="glucose" optional="false" label="Query" help="Type in a query for example glucose"/>
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26 </inputs>
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27 <outputs>
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28 <data format="txt" name="output" label="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="dbname" value="glycan" />
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37 <param name="searchpattern" value="gl:G00357" />
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38 <output name="output" file="find_test1.txt" />
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39 </test>
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40 </tests>
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41
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42 <help> <![CDATA[
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43 .. class:: infomark
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44
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45 **What this tool does**
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46
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47 This tool searches the KEGG database with your text query .
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48
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49 .. class:: infomark
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50
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51 **Input**
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52
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53 Text.
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54
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55 ----
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56
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57 .. class:: infomark
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58
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59 **Example**
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60
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61 Query sequence::
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62
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63 glucose
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64
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65 output sequence::
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66
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67 gl:G00357 Laminaribiose; Laminariobiose; 3-O-beta-D-Glucopyranosyl-D-glucose; (Glc)2; Glycolipid; Others Glycoprotein; O-Glycan Glycoside Polysaccharide
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68 gl:G10608 UDP-D-glucose; UDP-glucose; Uridine diphosphate glucose; (UDP-Glc)1
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69 gl:G11108 GDP-glucose; (GDP-Glc)1
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70 gl:G11109 ADP-glucose; Adenosine diphosphoglucose; (ADP-Glc)1
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71 gl:G11728 Acarviosine-glucose; (Avc)1 (Glc)1
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72
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73 ]]>
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74 </help>
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75
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76 </tool>
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