# HG changeset patch
# User rdvelazquez
# Date 1524154257 14400
# Node ID d91cbcdac691627a527361c6b0664d8be296c7eb
# Parent  2d9b98a2a0d63e6e5fde18b514a4bcc10c4c9519
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty

diff -r 2d9b98a2a0d6 -r d91cbcdac691 bealign.xml
--- a/bealign.xml	Wed Mar 14 14:44:06 2018 -0400
+++ b/bealign.xml	Thu Apr 19 12:10:57 2018 -0400
@@ -8,7 +8,10 @@
     <version_command>bealign --version</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-    bealign --reference '$select_reference.reference' $advanced.expected_identity --alphabet $advanced.alphabet
+    bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet
+        #if $advanced.expected_identity:
+            --expected-identity $advanced.expected_identity
+        #end if
         --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference
         #if $advanced.discard:
             $advanced.discard $advanced.discarded_reads
@@ -46,7 +49,7 @@
             </when>
         </conditional>
         <section name="advanced" title="Advanced options" expanded="False">
-            <param name="expected_identity" argument="--expected-identity" type="boolean" checked="False" truevalue="--expected-identity" falsevalue="" label="Discard sequences that are insufficiently identical to the reference" />
+            <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference" />
             <param argument="--alphabet" type="select" label="Alphabet to use for alignment">
                 <option value="codon" selected="True">Codon</option>
                 <option value="dna">DNA</option>
@@ -89,6 +92,14 @@
             <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
             <output name="output" file="bealign-out2.bam" />
         </test>
+        <test>
+            <param name="input" ftype="fasta" value="bealign-in2.fa" />
+            <param name="reference_type" value="dataset" />
+            <param name="expected_identity" value="0.9" />
+            <param name="score_matrix" value="BLOSUM62" />
+            <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />
+            <output name="output" file="bealign-out3.bam" />
+        </test>
     </tests>
     <help>
     <![CDATA[
@@ -118,7 +129,6 @@
   -v, --version         print version information and exit
   -K, --keep-reference  include the reference sequence as the first one in the
                         resulting BAM file [the default is to strip it]
-    ]]>
-    </help>
-    <expand macro="citations" />
+    ]]></help>
+  <expand macro="citations"/>
 </tool>
diff -r 2d9b98a2a0d6 -r d91cbcdac691 test-data/bealign-out3.bam
Binary file test-data/bealign-out3.bam has changed