diff tools/samtools_idxstats/samtools_idxstats.xml @ 1:8945bad80f4a draft

v0.0.4; internal changes for packaging

--- a/tools/samtools_idxstats/samtools_idxstats.xml	Wed Nov 20 12:27:33 2013 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.xml	Wed May 13 10:35:50 2015 -0400
@@ -1,9 +1,14 @@
-<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1">
+<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4">
     <description>samtools idxstats</description>
     <requirements>
         <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command interpreter="python">samtools_idxstats.py --version</version_command>
     <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
     <inputs>
@@ -12,11 +17,6 @@
     <outputs>
         <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" />
     </outputs>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <tests>
         <test>
             <param name="input_bam" value="ex1.bam" ftype="bam" />
@@ -73,4 +73,7 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
 </tool>