# HG changeset patch
# User iuc
# Date 1449396192 18000
# Node ID 8187a729d9f4ac5f52023b8169844497a598f76c
# Parent  4e4e4093d65d3c7377067f5d7499d454b228aca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841

diff -r 4e4e4093d65d -r 8187a729d9f4 bam_filter.xml
--- a/bam_filter.xml	Wed Nov 11 13:04:07 2015 -0500
+++ b/bam_filter.xml	Sun Dec 06 05:03:12 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@.0">
+<tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@.1">
     <description>Removes reads from a BAM file based on criteria</description>
     <macros>
         <import>macros.xml</import>
@@ -7,6 +7,7 @@
     <expand macro="stdio" />
     <expand macro="version" />
     <command><![CDATA[
+
     ## If the tool is executed with no filtering option,
     ## the default parameters simply copy over the input file
     if grep -q "\w" ${parameters};
@@ -18,6 +19,7 @@
     else
         cp $infile $outfile;
     fi
+
 ]]>
     </command>
     <configfiles>
@@ -34,7 +36,7 @@
         $properpair
         $noproperpair
         #if $mask:
-            -mask "${mask}"
+            -mask ${mask}
         #end if
         #if int($uniq) > -1:
             -uniq
@@ -50,16 +52,16 @@
         $noqcfail
         $nopcrdup
         #if $excludebed:
-            -excludebed "${excludebed}" $ignore_strand
+            -excludebed ${excludebed} $ignore_strand
         #end if
         #if $includebed:
-            -includebed "${includebed}" $ignore_strand
+            -includebed ${includebed} $ignore_strand
         #end if
         #if $includeref:
-            -includeref "${includeref}"
+            -includeref ${includeref}
         #end if
         #if $excluderef:
-            -excluderef "${excluderef}"
+            -excluderef ${excluderef}
         #end if
         #if $maximum_mismatch_ratio
             -maximum_mismatch_ratio $maximum_mismatch_ratio
@@ -116,8 +118,8 @@
         <param argument="-excludebed" type="data" optional="True" format="bed" label="Remove reads that are in any of the regions" />
         <param argument="-includebed" type="data" optional="True" format="bed" label="Remove reads that are NOT any of the regions" />
         <param name="ignore_strand" truevalue="nostrand" type="boolean" falsevalue=""
-            label="Strand information from BED file is ignored. Affects -excludebed and -includebed."
-            help="" />
+            label="Strand information from BED file is ignored"
+            help="Affects -excludebed and -includebed." />
 
         <param argument="-includeref" type="text" value="" optional="True" label="Exclude reads NOT mapped to a reference"
             help="" />
@@ -155,12 +157,18 @@
         </test>
         <test>
             <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
-            <output name="outfile" file="ngsutils_bam_filter_input1.bam" ftype="bam" />
+            <output name="outfile" file="ngsutils_bam_filter_input4.bam" ftype="bam" />
         </test>
         <test>
             <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
             <param name="mask" value="0x40"/>
-            <output name="outfile" file="ngsutils_bam_filter_result4.bam" ftype="bam" />
+            <output name="outfile" file="ngsutils_bam_filter_result5.bam" ftype="bam" />
+        </test>
+        <test>
+            <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
+            <param name="excludebed" value="exclude.bed" ftype="bed"/>
+            <param name="ignore_strand" value="True" />
+            <output name="outfile" file="ngsutils_bam_filter_result6.bam" ftype="bam" />
         </test>
     </tests>
     <help><![CDATA[
diff -r 4e4e4093d65d -r 8187a729d9f4 ngsutils/__init__.pyc
Binary file ngsutils/__init__.pyc has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 ngsutils/bam/__init__.pyc
Binary file ngsutils/bam/__init__.pyc has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 ngsutils/bed/__init__.pyc
Binary file ngsutils/bed/__init__.pyc has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 ngsutils/support/__init__.pyc
Binary file ngsutils/support/__init__.pyc has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 ngsutils/support/dbsnp.pyc
Binary file ngsutils/support/dbsnp.pyc has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 ngsutils/support/ngs_utils.pyc
Binary file ngsutils/support/ngs_utils.pyc has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 test-data/exclude.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclude.bed	Sun Dec 06 05:03:12 2015 -0500
@@ -0,0 +1,1 @@
+chrM	1000	16000
diff -r 4e4e4093d65d -r 8187a729d9f4 test-data/ngsutils_bam_filter_input4.bam
Binary file test-data/ngsutils_bam_filter_input4.bam has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 test-data/ngsutils_bam_filter_result5.bam
Binary file test-data/ngsutils_bam_filter_result5.bam has changed
diff -r 4e4e4093d65d -r 8187a729d9f4 test-data/ngsutils_bam_filter_result6.bam
Binary file test-data/ngsutils_bam_filter_result6.bam has changed