Mercurial > repos > gandres > readseq

changeset 4:1a40d002fdc4 draft default tip

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planemo upload
author gandres
date Wed, 15 Jun 2016 09:18:26 -0400
parents b38275a23ce0
children
files readseq.xml
diffstat 1 files changed, 19 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/readseq.xml	Fri Dec 11 09:23:33 2015 -0500
+++ b/readseq.xml	Wed Jun 15 09:18:26 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sniplay_readseq" name="Readseq" version="1.0.2">
+<tool id="sniplay_readseq" name="Readseq" version="1.0.3">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> Convert various alignment formats </description>
@@ -17,7 +17,6 @@
 
     <!-- [REQUIRED] The command to execute -->
     <command>
-	echo \$JAVA_JAR_PATH &amp;&amp;
 	java -jar \$JAVA_JAR_PATH/readseq.jar $filein -f $format >> $fileout_log 2>&amp;1 &amp;&amp;
 #if str( $format ) == "1":
  mv ${filein}.ig $fileout
@@ -84,7 +83,24 @@
     <!-- [REQUIRED] Output files -->
     <outputs>
 	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
-	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+	<data name="fileout" type="data" format="txt" label="${fileout_label}" >
+		<change_format>
+			<when input="format" value="1" format="ig" />
+			<when input="format" value="2" format="genbank" />
+			<when input="format" value="4" format="embl" />
+			<when input="format" value="5" format="gcg" />
+			<when input="format" value="6" format="strider" />
+			<when input="format" value="8" format="fasta" />
+			<when input="format" value="11" format="phylip" />
+			<when input="format" value="12" format="phylip" />
+			<when input="format" value="14" format="pir" />
+			<when input="format" value="17" format="nexus" />
+			<when input="format" value="18" format="prettyseq" />
+			<when input="format" value="19" format="xml" />
+			<when input="format" value="22" format="clustal" />
+			<when input="format" value="25" format="acedb" />
+		</change_format>
+	</data>
     </outputs>
     
     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->