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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/kegg_glycan/findKEGG.xml	Wed Mar 23 14:35:56 2016 -0400
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+<tool id="glytools_kegg_find" name="GAP Find KEGG glycans " version="0.3.1">
+    <description> using the KEGG  database</description>
+    <requirements>
+        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
+    </requirements> 
+    <command interpreter="python"><![CDATA[ findKEGG.py -d $dbname -q $searchpattern -o $output ]]></command>
+    <inputs>
+        <param name="dbname" type="select" label="Database">
+          <option value="glycan" selected="true"> search KEGG glycan database</option>
+          <option value="pathway" selected="false"> search KEGG pathway database</option>
+          <option value="brite" selected="false"> search KEGG brite database</option>
+          <option value="module" selected="false"> search KEGG module database</option>
+          <option value="ko" selected="false"> search KEGG ko database</option>
+          <option value="genome" selected="false"> search KEGG genome database</option>
+          <option value="compound" selected="false"> search KEGG compound database</option>
+          <option value="reaction" selected="false"> search KEGG reaction database</option>
+          <option value="rpair" selected="false"> search KEGG rpair database</option>
+          <option value="rclass" selected="false"> search KEGG rclass database</option>
+          <option value="enzyme" selected="false"> search KEGG enzyme database</option>
+          <option value="disease" selected="false"> search KEGG disease database</option>
+          <option value="drug" selected="false"> search KEGG drug database</option>
+          <option value="dgroup" selected="false"> search KEGG dgroup database</option>
+          <option value="environ" selected="false"> search KEGG environ database</option>
+        </param>
+        <param name="searchpattern" type="text" value="glucose" optional="false" label="Query" help="Type in a query for example glucose"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" label="entries from KEGG database search"/>
+    </outputs>
+ <citations>
+     <!--  -->
+     <citation type="doi">10.1002/0471250953.bi0112s38</citation>
+ </citations>
+ <tests>
+    <test>
+      <param name="dbname" value="glycan" />
+      <param name="searchpattern" value="gl:G00357" />
+      <output name="output" file="find_test1.txt" />     
+  </test>
+  </tests>
+
+    <help> <![CDATA[ 
+.. class:: infomark
+
+**What this tool does**
+
+This tool searches the KEGG database with your text query .
+
+.. class:: infomark
+
+**Input**
+
+Text.
+
+----
+
+.. class:: infomark
+
+**Example**
+
+Query sequence::
+
+ glucose
+
+output 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
+ gl:G11108       GDP-glucose; (GDP-Glc)1
+ gl:G11109       ADP-glucose; Adenosine diphosphoglucose; (ADP-Glc)1
+ gl:G11728       Acarviosine-glucose; (Avc)1 (Glc)1
+
+]]>
+</help>
+
+</tool>