Mercurial > repos > iuc > meme_fimo

diff fimo.xml @ 7:de3c73f58451 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
author iuc
date Sun, 10 Jul 2016 09:01:50 -0400
parents 3357222bd843
children b69b8c6bbbde
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--- a/fimo.xml	Thu Jul 07 09:53:04 2016 -0400
+++ b/fimo.xml	Sun Jul 10 09:01:50 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"/>