diff extract_aln_ends.xml @ 14:570a7de9f151 draft

read from bam; fix header issue

--- a/extract_aln_ends.xml	Fri Nov 27 04:33:02 2015 -0500
+++ b/extract_aln_ends.xml	Mon Nov 30 07:53:36 2015 -0500
@@ -14,7 +14,7 @@
 
 > $default]]></command>
   <inputs>
-    <param area="false" label="Sam input." name="positional_1" type="data" format="sam"/>
+    <param area="false" label="Alignments in SAM or BAM format." name="positional_1" type="data" format="sam,bam"/>
   </inputs>
   <outputs>
     <data format="bed" hidden="false" name="default"/>
@@ -26,7 +26,7 @@
     </test>
   </tests>
   <help><![CDATA[
-Extract alignment ends from sam file.
+Extract alignment ends from bam file.
 
 The resulting bed file contains the outer coordinates of the alignments. The
 bed name field is set to the read id and the score field is set to the edit
@@ -38,7 +38,7 @@
 
 Input:
 
-* sam file containing alignments (paired-end sequencing)
+* bam file containing alignments (paired-end sequencing)
 
 Output: