diff fimo.xml @ 8:53846f74a019 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf

--- a/fimo.xml	Thu Jul 07 09:55:00 2016 -0400
+++ b/fimo.xml	Sun Jul 10 09:02:14 2016 -0400
@@ -1,9 +1,16 @@
-<tool id="meme_fimo" name="FIMO" version="4.11.0.4">
+<tool id="meme_fimo" name="FIMO" version="4.11.1.0">
     <description>- Scan a set of sequences for motifs.</description>
     <requirements>
-        <requirement type="package" version="6.9.3">imagemagick</requirement>
-        <requirement type="package" version="4.11.0">meme</requirement>
+        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        <requirement type="package" version="4.11.1">meme</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command>
         <![CDATA[
             mkdir -p output &&
@@ -255,7 +262,7 @@
             <param name="fasta_type_selector" value="history"/>
             <param name="input_database" value="phiX.fasta" ftype="fasta"/>
             <param name="options_type_selector" value="advanced"/>
-            <param name="parse_genomic_coord" value="--parse_genomic_coord"/>
+            <param name="parse_genomic_coord" value="yes"/>
             <param name="remove_duplicate_coords" value="yes"/>
             <param name="output_separate_motifs" value="yes"/>
             <param name="non_commercial_use" value="True"/>