diff manipulate/rename_kcf/rename_kcf.xml @ 0:89592faa2875 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manipulate/rename_kcf/rename_kcf.xml	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,43 @@
+<tool id="glytools_rename_KCF" name="GAP Rename KCF" version="0.3">
+    <description>rename the ENTRY tag in KCF file</description>
+    <requirements>
+        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
+    </requirements> 
+    <command interpreter="python"><![CDATA[ rename_kcf.py -i $input -o $kcfoutput -p $prefix -c $counter]]></command>
+    <inputs>
+        <param format="kcf" name="input" type="data" label="KCF source file"/>
+        <param name="prefix" type="text" value="GLY" optional="false" label="Prefix for renaming ENTRY" help="Type in a prefix for renaming entry"/>
+        <param name="counter" type="integer" value="0" min="0" max="10000" optional="false" label="Integer start counter for renaming ENTRY"/>
+    </inputs>
+    <outputs>
+        <data format="kcf" name="kcfoutput" label="Renamed KCF $input.name"/>
+    </outputs>
+
+ <citations>
+     <!--  -->
+     <citation type="doi">10.1002/0471250953.bi0112s38</citation>
+  </citations>
+
+    <help> <![CDATA[ 
+.. class:: infomark
+
+**What this tool does**
+
+This tool reads KCF glycans and sequentially renames them as GLY{$COUNT}. Why? Sometimes entry names have illegal chars e.g. "-" or sometimes they are linearcode. Which seems great but linearcode is too long and has too many illegals chars in it, meaning that other tools along the pipeline start to fail. 
+
+.. class:: infomark
+
+**Input**
+
+*KCF*
+
+.. class:: infomark
+
+**Output**
+
+*KCF*
+
+]]>
+    </help>
+
+</tool>