Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/kegg_glycan/findKEGG.xml @ 0:89592faa2875 draft
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| author | chrisb |
|---|---|
| date | Wed, 23 Mar 2016 14:35:56 -0400 |
| parents | |
| children | 0a5e0df17054 |
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| -1:000000000000 | 0:89592faa2875 |
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| 1 <tool id="glytools_kegg_find" name="GAP Find KEGG glycans " version="0.3.1"> | |
| 2 <description> using the KEGG database</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"><![CDATA[ findKEGG.py -d $dbname -q $searchpattern -o $output ]]></command> | |
| 7 <inputs> | |
| 8 <param name="dbname" type="select" label="Database"> | |
| 9 <option value="glycan" selected="true"> search KEGG glycan database</option> | |
| 10 <option value="pathway" selected="false"> search KEGG pathway database</option> | |
| 11 <option value="brite" selected="false"> search KEGG brite database</option> | |
| 12 <option value="module" selected="false"> search KEGG module database</option> | |
| 13 <option value="ko" selected="false"> search KEGG ko database</option> | |
| 14 <option value="genome" selected="false"> search KEGG genome database</option> | |
| 15 <option value="compound" selected="false"> search KEGG compound database</option> | |
| 16 <option value="reaction" selected="false"> search KEGG reaction database</option> | |
| 17 <option value="rpair" selected="false"> search KEGG rpair database</option> | |
| 18 <option value="rclass" selected="false"> search KEGG rclass database</option> | |
| 19 <option value="enzyme" selected="false"> search KEGG enzyme database</option> | |
| 20 <option value="disease" selected="false"> search KEGG disease database</option> | |
| 21 <option value="drug" selected="false"> search KEGG drug database</option> | |
| 22 <option value="dgroup" selected="false"> search KEGG dgroup database</option> | |
| 23 <option value="environ" selected="false"> search KEGG environ database</option> | |
| 24 </param> | |
| 25 <param name="searchpattern" type="text" value="glucose" optional="false" label="Query" help="Type in a query for example glucose"/> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="txt" name="output" label="entries from KEGG database search"/> | |
| 29 </outputs> | |
| 30 <citations> | |
| 31 <!-- --> | |
| 32 <citation type="doi">10.1002/0471250953.bi0112s38</citation> | |
| 33 </citations> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="dbname" value="glycan" /> | |
| 37 <param name="searchpattern" value="gl:G00357" /> | |
| 38 <output name="output" file="find_test1.txt" /> | |
| 39 </test> | |
| 40 </tests> | |
| 41 | |
| 42 <help> <![CDATA[ | |
| 43 .. class:: infomark | |
| 44 | |
| 45 **What this tool does** | |
| 46 | |
| 47 This tool searches the KEGG database with your text query . | |
| 48 | |
| 49 .. class:: infomark | |
| 50 | |
| 51 **Input** | |
| 52 | |
| 53 Text. | |
| 54 | |
| 55 ---- | |
| 56 | |
| 57 .. class:: infomark | |
| 58 | |
| 59 **Example** | |
| 60 | |
| 61 Query sequence:: | |
| 62 | |
| 63 glucose | |
| 64 | |
| 65 output sequence:: | |
| 66 | |
| 67 gl:G00357 Laminaribiose; Laminariobiose; 3-O-beta-D-Glucopyranosyl-D-glucose; (Glc)2; Glycolipid; Others Glycoprotein; O-Glycan Glycoside Polysaccharide | |
| 68 gl:G10608 UDP-D-glucose; UDP-glucose; Uridine diphosphate glucose; (UDP-Glc)1 | |
| 69 gl:G11108 GDP-glucose; (GDP-Glc)1 | |
| 70 gl:G11109 ADP-glucose; Adenosine diphosphoglucose; (ADP-Glc)1 | |
| 71 gl:G11728 Acarviosine-glucose; (Avc)1 (Glc)1 | |
| 72 | |
| 73 ]]> | |
| 74 </help> | |
| 75 | |
| 76 </tool> |