| Previous changeset 4:d3292b4a0c78 (2016-07-27) Next changeset 6:dc6ff68ea5e8 (2017-10-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 |
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modified:
samtool_filter2.xml |
| b |
| diff -r d3292b4a0c78 -r b7aa423007bf samtool_filter2.xml --- 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> |