# HG changeset patch
# User iuc
# Date 1542712893 18000
# Node ID fdc58a0cc1d4ef03eea11db727ed0bc1b6bdb6bd
# Parent  b91e0f76afe98cdbca106122fb69bab5d414d6a3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d

diff -r b91e0f76afe9 -r fdc58a0cc1d4 samtools_view.xml
--- a/samtools_view.xml	Sun Oct 14 13:56:29 2018 -0400
+++ b/samtools_view.xml	Tue Nov 20 06:21:33 2018 -0500
@@ -41,7 +41,7 @@
         ## filter options (regions filter is the last parameter)
         #if $cond_filter.select_filter == 'yes':
             #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
-                -L '$cond_filter.bedfile'
+                -L '$cond_filter.cond_region.bedfile'
             #end if
             #if $cond_filter.cond_rg.select_rg == 'text':
                 -r '$cond_filter.cond_rg.readgr'
@@ -263,7 +263,7 @@
                 <when input="outtype" value="cram" format="cram" />
             </change_format>
         </data>
-        <data name="outputcnt" format="txt" from_work_dir="sam" label="${tool.name} on ${on_string}: Counts">
+        <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
             <filter>outtype == 'count'</filter>
         </data>
     </outputs>
@@ -312,6 +312,12 @@
             </conditional>
             <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
         </test>
+       <!-- count alignments -->
+       <test>
+            <param name="input" value="test.bam" ftype="bam" />
+            <param name="outtype" value="count" />
+            <output name="outputcnt" file="test_counts.tab" ftype="txt" />
+        </test>
         <test>
             <param name="input" value="test.sam" ftype="sam" />
             <param name="outtype" value="cram" />
@@ -425,7 +431,7 @@
                 <param name="seed" value="7" />
                 <param name="target" value="2" />
             </conditional>
-            <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" />
+            <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
         </test>
         <test>
             <param name="input" value="test.bam" ftype="bam" />
diff -r b91e0f76afe9 -r fdc58a0cc1d4 test-data/test_counts.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_counts.tab	Tue Nov 20 06:21:33 2018 -0500
@@ -0,0 +1,1 @@
+10