diff dexseq_count.xml @ 3:a26a82bed63f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96

--- a/dexseq_count.xml	Fri Sep 25 15:57:00 2015 -0400
+++ b/dexseq_count.xml	Fri Sep 25 16:26:39 2015 -0400
@@ -1,11 +1,18 @@
 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
     <requirements>
-        <requirement type="package" version="3.1.0">R</requirement>
-        <requirement type="package" version="1.14.2">dexseq</requirement>
+        <requirement type="package" version="1.14">dexseq</requirement>
         <requirement type="package" version="0.6.1">htseq</requirement>
-        <requirement type="package" version="0.7.6">pysam</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <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[
         #if $mode.mode_select == "prepare":
@@ -26,14 +33,6 @@
         #end if
     ]]>
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <!-- In case the return code has not been set propery check stderr too -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
     <inputs>
         <conditional name="mode">
             <param name="mode_select" type="select" label="Mode of operation">
@@ -66,10 +65,10 @@
 
     <outputs>
         <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
-            <filter>(mode['mode_select'] == 'count')</filter>
+            <filter>mode['mode_select'] == 'count'</filter>
         </data>
-        <data format="gff" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}">
-            <filter>(mode['mode_select'] == 'prepare')</filter>
+        <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}">
+            <filter>mode['mode_select'] == 'prepare'</filter>
         </data>
     </outputs>