diff idxml_to_tabular.xml @ 4:1183846e70a1 draft

Uploaded

--- a/idxml_to_tabular.xml	Fri May 10 17:31:59 2013 -0400
+++ b/idxml_to_tabular.xml	Wed Jun 19 13:15:44 2013 -0400
@@ -14,23 +14,18 @@
     <configfile name="config">[simple_options]
 in=${in}
 out=${out}
-#if $dump_type == "protein"
-proteins_only=true
-#end if
-#if $dump_type == "pepetide"
-peptides_only=true
-#end if
-$extra_rt
+$dump_type
+id!first_dim_rt=$extra_rt
 </configfile>
   </configfiles>
   <inputs>
     <param format="idxml" name="in" type="data" label="Input Identification File"/>
     <param name="dump_type" type="select" label="Export type">
-      <option value="all">Run, peptide, and protein information</option>
-      <option value="protein">Run and protein information only</option>
-      <option value="peptide">Peptide information only</option>
+      <option value="">Run, peptide, and protein information</option>
+      <option value="id!proteins_only=true">Run and protein information only</option>
+      <option value="id!peptides_only=true">Peptide information only</option>
     </param>
-    <param name="extra_rt" type="boolean" truevalue="first_dim_rt=true" falsevalue="" label="Include RT information (if present)" />
+    <param name="extra_rt" type="boolean" label="Include RT information (if present)" />
   </inputs>
   <outputs>
     <data format="tabular" name="out">