Mercurial > repos > iuc > ngsutils_bam_filter
changeset 1:a0264bbe8682 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 4a7736168ec93adb93e6c7d21d80b201ea5c5352-dirty
| author | iuc |
|---|---|
| date | Tue, 10 Nov 2015 15:08:52 -0500 |
| parents | 60115871d49e |
| children | 4ce5e195f496 |
| files | bam_filter.xml test-data/ngsutils_bam_filter_result2.bam test-data/ngsutils_bam_filter_result3.bam |
| diffstat | 3 files changed, 52 insertions(+), 37 deletions(-) [+] |
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--- a/bam_filter.xml Tue Nov 10 14:35:04 2015 -0500 +++ b/bam_filter.xml Tue Nov 10 15:08:52 2015 -0500 @@ -7,7 +7,6 @@ <expand macro="stdio" /> <expand macro="version" /> <command><![CDATA[ - pip install eta && $__tool_directory__/filter.py $infile $outfile @@ -141,7 +140,7 @@ <param name="nosecondary" value="True"/> <param name="noqcfail" value="True"/> <param name="nopcrdup" value="True"/> - <output name="outfile" file="ngsutils_bam_filter_result2.bam" ftype="bam" /> + <output name="outfile" file="ngsutils_bam_filter_result3.bam" ftype="bam" /> </test> </tests> <help><![CDATA[ @@ -156,42 +155,58 @@ filtering, the IH:i tag would still read IH:i:2). Currently, the available filters are: - * -minlen val Remove reads that are smaller than {val} - * -maxlen val Remove reads that are larger than {val} - * -mapped Keep only mapped reads - * -unmapped Keep only unmapped reads - * -properpair Keep only properly paired reads (both mapped, - correct orientation, flag set in BAM) - * -noproperpair Keep only not-properly paired reads - * -mask bitmask Remove reads that match the mask (base 10/hex) - * -uniq {length} Remove reads that are have the same sequence - Note: BAM file should be sorted - (up to an optional length) - * -uniq_start Remove reads that start at the same position - Note: BAM file should be sorted - (Use only for low-coverage samples) - * -mismatch num # mismatches or indels - indel always counts as 1 regardless of length - (requires NM tag in reads) - * -nosecondary Remove reads that have the 0x100 flag set - * -noqcfail Remove reads that have the 0x200 flag set - * -nopcrdup Remove reads that have the 0x400 flag set - * -excludebed file.bed {nostrand} - Remove reads that are in any of the regions - from the given BED file. If 'nostrand' is given, - strand information from the BED file is ignored. - * -includebed file.bed {nostrand} - Remove reads that are NOT any of the regions - from the given BED file. If 'nostrand' is given, - strand information from the BED file is ignored. - - Note: If this is a large dataset, use - "bamutils extract" instead. - * -includeref refname Exclude reads NOT mapped to a reference - * -excluderef refname Exclude reads mapped to a particular reference - (e.g. chrM, or _dup chromosomes) - ++--------------------------------+-------------------------------------------------+ +| Agument | Description | ++================================+=================================================+ +| -minlen val | Remove reads that are smaller than {val} | ++--------------------------------+-------------------------------------------------+ +| -maxlen val | Remove reads that are larger than {val} | ++--------------------------------+-------------------------------------------------+ +| -mapped | Keep only mapped reads | ++--------------------------------+-------------------------------------------------+ +| -unmapped | Keep only unmapped reads | ++--------------------------------+-------------------------------------------------+ +| -properpair | Keep only properly paired reads (both mapped, | +| | correct orientation, flag set in BAM) | ++--------------------------------+-------------------------------------------------+ +| -noproperpair | Keep only not-properly paired reads | ++--------------------------------+-------------------------------------------------+ +| -mask bitmask | Remove reads that match the mask (base 10/hex) | ++--------------------------------+-------------------------------------------------+ +| -uniq {length} | Remove reads that are have the same sequence | +| | Note: BAM file should be sorted | +| | (up to an optional length) | ++--------------------------------+-------------------------------------------------+ +| -uniq_start | Remove reads that start at the same position | +| | Note: BAM file should be sorted | +| | (Use only for low-coverage samples) | ++--------------------------------+-------------------------------------------------+ +|-mismatch num | Number of mismatches or indels | +| | indel always counts as 1 regardless of length | +| | (requires NM tag in reads) | ++--------------------------------+-------------------------------------------------+ +|-nosecondary | Remove reads that have the 0x100 flag set | ++--------------------------------+-------------------------------------------------+ +|-noqcfail | Remove reads that have the 0x200 flag set | ++--------------------------------+-------------------------------------------------+ +|-nopcrdup | Remove reads that have the 0x400 flag set | ++--------------------------------+-------------------------------------------------+ +|-excludebed file.bed {nostrand} | Remove reads that are in any of the regions | +| | from the given BED file. If 'nostrand' is given,| +| | strand information from the BED file is ignored.| ++--------------------------------+-------------------------------------------------+ +|-includebed file.bed {nostrand} | Remove reads that are NOT any of the regions | +| | from the given BED file. If 'nostrand' is given,| +| | strand information from the BED file is ignored.| +| | Note: If this is a large dataset, use | +| | "bamutils extract" instead. | ++--------------------------------+-------------------------------------------------+ +| -includeref refname | Exclude reads NOT mapped to a reference | ++--------------------------------+-------------------------------------------------+ +| -excluderef refname | Exclude reads mapped to a particular reference | +| | (e.g. chrM, or _dup chromosomes) | ++--------------------------------+-------------------------------------------------+ ]]> </help> </tool>