diff samtools_phase.xml @ 3:c21cb56fbbbc draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/samtools_phase.xml	Fri Sep 26 15:20:35 2014 -0400
+++ b/samtools_phase.xml	Tue Oct 13 12:55:05 2015 -0400
@@ -1,8 +1,11 @@
-<tool id="samtools_phase" name="Call and phase" version="1.0.2">
+<tool id="samtools_phase" name="Call and phase" version="2.0">
     <description>heterozygous SNPs</description>
-    <requirements>
-        <requirement type="package" version="1.1">samtools</requirement>
-    </requirements>
+    <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
     <command>samtools phase -b "phase_wrapper"
         #if str($option_set.option_sets) == 'advanced':
             ${option_set.ignore_chimeras}
@@ -16,9 +19,6 @@
         #end if
         "$input_bam" &gt; "$phase_sets"
     </command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Error" />
-    </stdio>
     <inputs>
         <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
         <conditional name="option_set">
@@ -125,14 +125,6 @@
      - Drop reads with ambiguous phase
      - *off*
 
-------
-
-**Citation**
-
-For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
-
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-        </help>
+    </help>
+    <expand macro="citations"></expand>
 </tool>