diff get_data/kegg_glycan/linkKEGG.xml @ 0:89592faa2875 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/kegg_glycan/linkKEGG.xml	Wed Mar 23 14:35:56 2016 -0400
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+<tool id="glytools_kegg_link" name="GAP Cross-reference with KEGG databases " version="0.3.1">
+    <description> searches KEGG for related database entries</description>
+    <requirements>
+        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
+    </requirements> 
+    <command interpreter="python"><![CDATA[linkKEGG.py -t $targetdb -s $source -o $output ]]></command>
+    <inputs>
+        <param name="targetdb" type="select" label="Target Database">
+          <option value="glycan" selected="true"> target KEGG glycan database</option>
+          <option value="pathway" selected="false"> target KEGG pathway database</option>
+          <option value="brite" selected="false"> target KEGG brite database</option>
+          <option value="module" selected="false"> target KEGG module database</option>
+          <option value="ko" selected="false"> target KEGG ko database</option>
+          <option value="genome" selected="false"> target KEGG genome database</option>
+          <option value="compound" selected="false"> target KEGG compound database</option>
+          <option value="reaction" selected="false"> target KEGG reaction database</option>
+          <option value="rpair" selected="false"> target KEGG rpair database</option>
+          <option value="rclass" selected="false"> target KEGG rclass database</option>
+          <option value="enzyme" selected="false"> target KEGG enzyme database</option>
+          <option value="disease" selected="false"> target KEGG disease database</option>
+          <option value="drug" selected="false"> target KEGG drug database</option>
+          <option value="dgroup" selected="false"> target KEGG dgroup database</option>
+          <option value="environ" selected="false"> target KEGG environ database</option>
+        </param>
+        <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"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" label="linked entries from KEGG database search"/>
+    </outputs>
+ <citations>
+     <!--  -->
+     <citation type="doi">10.1002/0471250953.bi0112s38</citation>
+  </citations>
+ <tests>
+    <test>
+      <param name="targetdb" value="glycan" />
+      <param name="source" value="ec:2.4.1.11"" />
+      <output name="output" file="link_test1.txt" />     
+  </test>
+  </tests>
+    <help> <![CDATA[ 
+.. class:: infomark
+
+**What this tool does**
+
+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,
+or which glycans are acted by an enzyme that acts on UDP-Glucose (ec:2.4.1.11).
+
+----
+
+.. class:: infomark
+
+**Example 1**
+
+target and source sequence::
+
+ enzyme
+ gl:G10608 
+
+output sequence::
+
+ gl:G10608    ec:2.4.1.11
+ gl:G10608    ec:2.4.1.12
+ gl:G10608    ec:2.4.1.13
+ gl:G10608    ec:2.4.1.14
+ gl:G10608    ec:2.4.1.15
+ gl:G10608    ec:2.4.1.183
+ gl:G10608    ec:2.4.1.188
+ gl:G10608    ec:2.4.1.34
+ gl:G10608    ec:2.4.1.53
+ gl:G10608    ec:2.4.1.80
+ 
+.. class:: infomark
+
+**Example 2**
+
+target and source sequence::
+
+ reaction
+ gl:G10608 
+
+output sequence::
+
+ gl:G10608    rn:R06020
+ gl:G10608    rn:R06023
+ gl:G10608    rn:R06036
+ gl:G10608    rn:R06043
+ gl:G10608    rn:R06045
+ gl:G10608    rn:R06051
+ gl:G10608    rn:R06062
+ gl:G10608    rn:R06073
+ gl:G10608    rn:R06181
+ gl:G10608    rn:R06226
+ gl:G10608    rn:R06275
+ gl:G10608    rn:R09315
+ gl:G10608    rn:R09316
+
+.. class:: infomark
+
+**Example 3**
+
+target and source sequence::
+
+ glycan
+ ec:2.4.1.11
+
+output sequence::
+
+ ec:2.4.1.11    gl:G10495
+ ec:2.4.1.11    gl:G10608
+ ec:2.4.1.11    gl:G10619
+
+]]>
+
+</help>
+
+</tool>