diff idconvert.xml @ 0:4f7d6bec667f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idconvert.xml	Fri Apr 08 16:07:32 2016 -0400
@@ -0,0 +1,49 @@
+<tool id="idconvert" name="idconvert" version="@VERSION@.0">
+    <description>Convert mass spectrometry identification files</description>
+
+    <macros>
+        <import>msconvert_macros.xml</import>
+    </macros>
+
+    <expand macro="generic_requirements" />
+
+    <command>
+<![CDATA[
+#set input_name 
+ln -s $input input.${input.extension}
+idconvert input 
+
+]]>
+    </command>
+
+    <inputs> 
+        <conditional name="from">
+            <param name="from_format" type="select" label="Convert from">
+                <option value="mzid">mzIdentML (mzid)</option>
+                <option value="protxml">protXML (protxml)</option>
+                <option value="pepxml">pepXML (pepxml)</option>
+            </param>
+            <when value="mzid">
+                <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
+            </when>
+            <when value="protxml">
+                <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
+                <param name="pepxml" type="data" format="pepxml" label="MS Identification" />
+            </when>
+            <when value="pepxml">
+                <param name="input" type="data" format="pepxml" label="MS Identification" />
+            </when>
+        </conditional>
+        <param name="to_format" type="select" label="Convert to">
+            <option value="mzid">mzIdentML (mzid)</option>
+            <option value="pepxml">pepXML (pepxml)</option>
+            <option value="text">text</option>
+        </param>
+  </inputs>
+
+  <tests>
+  </tests>
+  <help>
+  </help>
+  <expand macro="citations" />
+</tool>