changeset 5:b7aa423007bf draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1

--- a/samtool_filter2.xml	Wed Jul 27 15:16:29 2016 -0400
+++ b/samtool_filter2.xml	Fri Jan 20 04:51:36 2017 -0500
@@ -9,38 +9,38 @@
   <command>
 <![CDATA[
 ##set up input files, regions requires input.bam and input.bai
-#if isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__):
+#if $input1.is_of_type('bam')
   #set $input = 'input.bam'
-  ln -s "$input1" $input &&
-  ln -s "$input1.metadata.bam_index" input.bai &&
-#elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__):
+  ln -s '$input1' $input &&
+  ln -s '$input1.metadata.bam_index' input.bai &&
+#elif $input1.is_of_type('sam')
   #set $input = 'input.sam'
-  ln -s "$input1" $input &&
+  ln -s '$input1' $input &&
 #end if
-samtools view $possibly_select_inverse "$output1" $header
+samtools view $possibly_select_inverse '$output1' $header
 
-  #if $input1.datatype.file_ext == 'sam':
+  #if $input1.is_of_type('sam')
    -S
   #end if
 
-  #if $outputtype.__str__ == "bam":
+  #if str($outputtype) == 'bam'
       -b
   #end if
 
-  #if $mapq.__str__ != '':
+  #if str($mapq)
    -q $mapq
   #end if
-  #if $flag.filter.__str__ == 'yes':
-   #if $flag.reqBits.__str__ != 'None':
-     #set $reqs = $flag.reqBits.__str__.split(',')
+  #if $flag.filter == 'yes'
+   #if str($flag.reqBits) != 'None'
+     #set $reqs = str($flag.reqBits).split(',')
      #set $reqFlag = 0
      #for $xn in $reqs:
-       #set $reqFlag += int(xn,16)
+       #set $reqFlag += int($xn, 16)
      #end for
      -f $hex($reqFlag)
    #end if
-   #if $flag.skipBits.__str__ != 'None':
-     #set $skips = $flag.skipBits.__str__.split(',')
+   #if str($flag.skipBits) != 'None'
+     #set $skips = str($flag.skipBits).split(',')
      #set $skipFlag = 0
      #for $xn in $skips:
        #set $skipFlag += int(xn,16)
@@ -48,18 +48,18 @@
      -F $hex($skipFlag)
    #end if
   #end if
-  #if $read_group.__str__.strip() != '':
-    -r $read_group
+  #if str($read_group).strip()
+    -r '$read_group'
   #end if
-  #if $library.__str__.strip() != '':
-    -l $library
+  #if str($library).strip()
+    -l '$library'
   #end if
-  #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0:
-    -L "$bed_file"
+  #if $bed_file
+    -L '$bed_file'
   #end if
   $input
-  #if $regions.__str__.strip() != '' and $input1.datatype.file_ext == 'bam':
-    $regions.__str__.strip()
+  #if str($regions).strip() and $input1.is_of_type('bam')
+    '$regions'
   #end if
   ## need to redirect stderr message so galaxy does not think this failed
   2>&1
@@ -206,7 +206,7 @@
 
 
 
-.. _SAMtools: http://samtools.sourceforge.net/
+.. _SAMtools: http://www.htslib.org/
 
   </help>
 </tool>