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1 <tool id="glytools_kegg_get" name="GAP Get KEGG glycans " version="0.3">
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2 <description> download kcf entries from KEGG</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[ getkcfKEGG.py -i $input -k $kcfout -d $dbout ]]></command>
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7 <inputs>
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8 <param format="txt" name="input" type="data" label="single or double column text file containing GL entries"/>
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9 </inputs>
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10 <outputs>
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11 <data format="kcf" name="kcfout" label="KEGG kcf output for $input.name"/>
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12 <data format="txt" name="dbout" label="KEGG db entry - $input.name"/>
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13 </outputs>
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14 <citations>
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15 <!-- -->
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16 <citation type="doi">10.1002/0471250953.bi0112s38</citation>
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17 </citations>
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18 <help> <![CDATA[
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19 .. class:: infomark
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20
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21 **What this tool does**
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22
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23 This tool will return both KCF and a text version of the KEGG database entry.
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24
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25 .. class:: infomark
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26
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27 **Input**
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28
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29 Text containing GL entries, for example as returned by a KEGG find result from the glycan DB.
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30
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31 ----
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32
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33 .. class:: infomark
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34
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35 **Example**
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36
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37 Query sequence::
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38
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39 gl:G00357 Laminaribiose; Laminariobiose; 3-O-beta-D-Glucopyranosyl-D-glucose; (Glc)2; Glycolipid; Others Glycoprotein; O-Glycan Glycoside Polysaccharide
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40 gl:G10608 UDP-D-glucose; UDP-glucose; Uridine diphosphate glucose; (UDP-Glc)1
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41
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42 kcf output sequence::
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43
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44 ENTRY G00357 Glycan
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45 NODE 2
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46 1 Glc 0 0
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47 2 Glc -10 0
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48 EDGE 1
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49 1 2:b1 1:3
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50 ///
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51 ENTRY G10608 Glycan
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52 NODE 1
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53 1 UDP-Glc -0.3 0
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54 EDGE 0
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55 ///
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56
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57 db output sequence::
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58
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59 ENTRY G00357 Glycan
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60 NAME Laminaribiose;
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61 Laminariobiose;
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62 3-O-beta-D-Glucopyranosyl-D-glucose
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63 COMPOSITION (Glc)2
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64 MASS 342.3
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65 CLASS Glycolipid; Others
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66 Glycoprotein; O-Glycan
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67 Glycoside
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68 Polysaccharide
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69 REMARK Same as: C02048
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70 REACTION R06058
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71 ENZYME 2.4.1.31
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72 DBLINKS CCSD: 3178 12230 17443 23581 28110 31447 32478 34039 36773 37192 38902 39794 39796 39797 39802 39804 40258 41633 41704 43790 44865 45671 47897 48035 48399
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73 GlycomeDB: 2361
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74 JCGGDB: JCGG-STR014653
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75 NODE 2
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76 1 Glc 0 0
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77 2 Glc -10 0
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78 EDGE 1
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79 1 2:b1 1:3
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80 ///
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81 ENTRY G10608 Glycan
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82 NAME UDP-D-glucose;
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83 UDP-glucose;
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84 Uridine diphosphate glucose
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85 COMPOSITION (UDP-Glc)1
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86 REMARK Same as: C00029
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87 REACTION R06020 R06023 R06036 R06043 R06045 R06051 R06062 R06073
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88 R06181 R06226 R06275 R09315 R09316
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89 ENZYME 2.4.1.11 2.4.1.12 2.4.1.13 2.4.1.14
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90 2.4.1.15 2.4.1.34 2.4.1.53 2.4.1.80
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91 2.4.1.183 2.4.1.188 2.4.1.-
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92 NODE 1
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93 1 UDP-Glc -0.3 0
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94 EDGE 0
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95
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96 ///
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97
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98 ]]>
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99 </help>
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100
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101 </tool>
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