# HG changeset patch
# User rdvelazquez
# Date 1524154292 14400
# Node ID c7c46222ee0ce7820ac34483f16425f1956455fb
# Parent  72b7678b5b09b63832ffa9a4784fc4e487a931a8
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty

diff -r 72b7678b5b09 -r c7c46222ee0c bam2msa.xml
--- a/bam2msa.xml	Wed Mar 14 14:46:48 2018 -0400
+++ b/bam2msa.xml	Thu Apr 19 12:11:32 2018 -0400
@@ -1,37 +1,35 @@
 <?xml version="1.0"?>
 <tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
-    <description>to FASTA multiple sequence alignment</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code">
-    <![CDATA[
+  <description>to FASTA multiple sequence alignment</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
     bam2msa
         #if $region_start and $region_end:
             -r $region_start:$region_end
         #end if
-        $input $output
-    ]]>
-    </command>
-    <inputs>
-        <param name="input" type="data" format="bam,sam" label="Input BAM file" />
-        <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences" />
-        <param name="region_end" type="integer" value="0" optional="True" label="End coordinate" />
-    </inputs>
-    <outputs>
-        <data name="output" format="fasta" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" ftype="bam" value="bealign-out1.bam" />
-            <output name="output" file="bam2msa-out1.fa" />
-        </test>
-        <test>
-            <param name="input" ftype="bam" value="bealign-out2.bam" />
-            <output name="output" file="bam2msa-out2.fa" />
-        </test>
-    </tests>
-    <help>Extract MSA from a BAM file</help>
-    <expand macro="citations" />
+        '$input' '$output'
+    ]]></command>
+  <inputs>
+    <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
+    <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
+    <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" ftype="bam" value="bealign-out1.bam"/>
+      <output name="output" file="bam2msa-out1.fa"/>
+    </test>
+    <test>
+      <param name="input" ftype="bam" value="bealign-out2.bam"/>
+      <output name="output" file="bam2msa-out2.fa"/>
+    </test>
+  </tests>
+  <help>Extract MSA from a BAM file</help>
+  <expand macro="citations"/>
 </tool>
diff -r 72b7678b5b09 -r c7c46222ee0c test-data/bealign-out3.bam
Binary file test-data/bealign-out3.bam has changed