# HG changeset patch
# User rdvelazquez
# Date 1553274183 14400
# Node ID f7866771310abf3cd6f05e11efdd12c09290dd95
# Parent  85d823cf087288875f2954d7ba04b08fd33ee1fe
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty

diff -r 85d823cf0872 -r f7866771310a bealign.xml
--- a/bealign.xml	Fri Mar 22 11:42:49 2019 -0400
+++ b/bealign.xml	Fri Mar 22 13:03:03 2019 -0400
@@ -13,6 +13,9 @@
             --expected-identity $advanced.expected_identity
         #end if
         --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
+        #if $advanced.discard:
+            --discard '$discarded_reads'
+        #end if
         '$input' '$output'
     ]]></command>
   <inputs>
@@ -66,6 +69,7 @@
         <option value="PAM250">PAM 250 substitution</option>
         <option value="HIV_BETWEEN_F">HIV between+F</option>
       </param>
+      <param name="discard" argument="--discard" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Output discarded sequences to a separate dataset"/>
       <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference"/>
       <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM"/>
     </section>