diff convert_detect_formats/rings_convert_format/glycan_convert.xml @ 0:89592faa2875 draft

Uploaded
author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_detect_formats/rings_convert_format/glycan_convert.xml	Wed Mar 23 14:35:56 2016 -0400
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+<tool id="glytools_converter_soap" name="GAP convert format (SOAP)" version="0.3">
+    <description> Convert between multiple glycan formats using the RINGS SOAP service</description>
+    <requirements>
+        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
+    </requirements> 
+    <command interpreter="python"><![CDATA[glycan_convert.py -i $input -f $changeformat -o $output]]></command>
+    <inputs>
+        <param format="kcf,glycoct_xml,linucs,linearcode,iupac,glydeii,txt" name="input" type="data" label="Source file"/>
+        <param name="changeformat" type="select" label="Format to convert to">
+          <option value="KCF" selected="true"> KCF </option>
+          <option value="LinearCode" selected="false"> LinearCode </option>
+          <option value="LINUCS" selected="false"> LINUCS </option>
+          <option value="GlycoCT" selected="false"> Glycoct </option>
+          <option value="IUPAC" selected="false"> IUPAC </option>
+        </param>
+    </inputs>
+    <outputs>
+
+        <data format="input" name="output" metadata_source="input">
+            <change_format>
+                <when input="changeformat" value="KCF" format="kcf"/>
+                <when input="changeformat" value="GlycoCT" format="glycoct"/>
+                <when input="changeformat" value="LinearCode" format="linearcode"/>
+                <when input="changeformat" value="IUPAC" format="iupac"/>
+                <when input="changeformat" value="LINUCS" format="linucs"/>
+            </change_format>
+        </data>
+    </outputs>
+
+ <citations>
+     <!--  -->
+     <citation type="doi">10.1089/omi.2009.0129</citation>
+</citations>
+
+    <help> <![CDATA[ 
+.. class:: infomark
+
+**What this tool does**
+
+This tool converts between glycan formats using the RINGS SOAP convert service.
+
+.. class:: infomark
+
+**Input**
+
+Any glycan dataset *except* for GlycoCT{condensed}, WURCS, MDL Mol and LINUCS (LINUCS only converts to LINUCS with this tools and the other formats do not convert)
+
+
+.. class:: infomark
+
+**Output**
+
+Can only convert to KCF, GlycoCT (xml), LinearCode, LINUCS, IUPAC  (last checked 25/02/2015).
+
+]]>
+    </help>
+
+</tool>