diff CRAPomeQuery.xml @ 11:659644782ecd draft

Uploaded

--- a/CRAPomeQuery.xml	Tue Apr 19 11:16:44 2016 -0400
+++ b/CRAPomeQuery.xml	Tue Apr 19 11:19:32 2016 -0400
@@ -15,6 +15,10 @@
     <data format="txt" name="CrapomeFile" label="CRAPome File"/>    
   </outputs>
   <stdio>
+    <regex match="TypeError"
+           source="stderr"
+           level="fatal"
+           description="Error: Check input file."/>
     <regex match="Error|error"
      source="stdout"
            level="fatal"
@@ -23,10 +27,6 @@
      source="stderr"
            level="fatal"
            description="Unknown error"/>
-    <regex match="Error: bad bait"
-           source="stdout"
-           level="fatal"
-           description="Error: bad bait"/>
   </stdio> 
   <tests>
     <test>
@@ -40,9 +40,11 @@
 This program will read in a SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions (e.g. "P00533" or "EGFR_HUMAN"), query the  CRAPome database (v1.1) http://crapome.org, and return a file specifying the prevalence of each protein in the CRAPome.
 
 **1) Input File**
+
 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.
 
 **2) Species**
+
 Please specify species. Supported species are Human and Yeast.
   </help>
 </tool>
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