Mercurial > repos > chrisb > gap_all_glycan_tools

<tool id="glytools_kegg_get" name="GAP Get KEGG glycans " version="0.3">
    <description> download kcf entries from KEGG</description>
    <requirements>
        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
    </requirements>
    <command interpreter="python"><![CDATA[ getkcfKEGG.py -i $input -k $kcfout -d $dbout ]]></command>
    <inputs>
        <param format="txt" name="input" type="data"  label="single or double column text file containing GL entries"/>
    </inputs>
    <outputs>
        <data format="kcf" name="kcfout" label="KEGG kcf output for $input.name"/>
        <data format="txt" name="dbout" label="KEGG db entry - $input.name"/>
    </outputs>
 <citations>
     <!--  -->
     <citation type="doi">10.1002/0471250953.bi0112s38</citation>
  </citations>
    <help> <![CDATA[
.. class:: infomark

**What this tool does**

This tool will return both KCF and a text version of the KEGG database entry.

.. class:: infomark

**Input**

Text containing GL entries, for example as returned by a KEGG find result from the glycan DB.

----

.. class:: infomark

**Example**

Query sequence::

 gl:G00357       Laminaribiose; Laminariobiose; 3-O-beta-D-Glucopyranosyl-D-glucose; (Glc)2; Glycolipid; Others Glycoprotein; O-Glycan Glycoside Polysaccharide
 gl:G10608       UDP-D-glucose; UDP-glucose; Uridine diphosphate glucose; (UDP-Glc)1

kcf output sequence::

 ENTRY       G00357                      Glycan
 NODE        2
             1   Glc         0     0
             2   Glc       -10     0
 EDGE        1
             1     2:b1    1:3
 ///
 ENTRY       G10608                      Glycan
 NODE        1
             1   UDP-Glc  -0.3     0
 EDGE        0
 ///

db output sequence::

 ENTRY       G00357                      Glycan
 NAME        Laminaribiose;
             Laminariobiose;
             3-O-beta-D-Glucopyranosyl-D-glucose
 COMPOSITION (Glc)2
 MASS        342.3
 CLASS       Glycolipid; Others
             Glycoprotein; O-Glycan
             Glycoside
             Polysaccharide
 REMARK      Same as: C02048
 REACTION    R06058
 ENZYME      2.4.1.31
 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
             GlycomeDB: 2361
             JCGGDB: JCGG-STR014653
 NODE        2
             1   Glc         0     0
             2   Glc       -10     0
 EDGE        1
             1     2:b1    1:3
 ///
 ENTRY       G10608                      Glycan
 NAME        UDP-D-glucose;
             UDP-glucose;
             Uridine diphosphate glucose
 COMPOSITION (UDP-Glc)1
 REMARK      Same as: C00029
 REACTION    R06020 R06023 R06036 R06043 R06045 R06051 R06062 R06073
             R06181 R06226 R06275 R09315 R09316
 ENZYME      2.4.1.11        2.4.1.12        2.4.1.13        2.4.1.14
             2.4.1.15        2.4.1.34        2.4.1.53        2.4.1.80
             2.4.1.183       2.4.1.188       2.4.1.-
 NODE        1
             1   UDP-Glc  -0.3     0
             EDGE        0

 ///

]]>
</help>

</tool>
author	chrisb
date	Fri, 06 May 2016 08:05:48 -0400
parents	89592faa2875
children