Mercurial > repos > iuc > ngsutils_bam_filter
changeset 2:4ce5e195f496 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
| author | iuc |
|---|---|
| date | Wed, 11 Nov 2015 13:03:30 -0500 |
| parents | a0264bbe8682 |
| children | 954ad23300ce |
| files | bam_filter.xml macros.xml ngsutils/__init__.pyc ngsutils/bam/__init__.pyc ngsutils/bed/__init__.pyc ngsutils/support/__init__.pyc ngsutils/support/dbsnp.pyc ngsutils/support/ngs_utils.pyc test-data/ngsutils_bam_filter_result4.bam |
| diffstat | 9 files changed, 46 insertions(+), 26 deletions(-) [+] |
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--- a/bam_filter.xml Tue Nov 10 15:08:52 2015 -0500 +++ b/bam_filter.xml Wed Nov 11 13:03:30 2015 -0500 @@ -7,9 +7,22 @@ <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}; + then $__tool_directory__/filter.py $infile $outfile + `cat ${parameters}`; + else + cp $infile $outfile; + fi +]]> + </command> + <configfiles> + <configfile name="parameters"> +<![CDATA[ #if $minlen: -minlen $minlen #end if @@ -21,7 +34,7 @@ $properpair $noproperpair #if $mask: - -mask $mask + -mask "${mask}" #end if #if int($uniq) > -1: -uniq @@ -30,7 +43,6 @@ #end if #end if $uniq_start - #if $mismatch: -mismatch $mismatch #end if @@ -38,24 +50,25 @@ $noqcfail $nopcrdup #if $excludebed: - -excludebed $ignore_strand + -excludebed "${excludebed}" $ignore_strand #end if #if $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 #end if -]]> - </command> + ]]> + </configfile> + </configfiles> <inputs> - <param name="infile" type="data" format="bam" label="Select SAM/BAM dataset" /> + <param name="infile" type="data" format="bam" label="Select BAM dataset" /> <param argument="-minlen" type="integer" value="" optional="True" min="0" label="Remove reads that are smaller than" help="in bp"/> @@ -72,14 +85,15 @@ label="Keep only properly paired reads" help="both mapped, correct orientation, flag set in BAM" /> <param argument="-noproperpair" truevalue="-noproperpair" type="boolean" falsevalue="" - label="Keep only not-properly paired reads" + label="Discard properly paired reads" help="" /> <param argument="-mask" type="text" value="" optional="True" label="Remove reads that match the mask" - help="base 10/hex based" /> + help="e.g. 0x400, 0x2" /> <param argument="-uniq" type="integer" value="-1" optional="True" min="-1" label="Remove reads that have the same sequence" - help="up to an optional length. -1 means do not filter and 0 means check the entire sequence for uniqueness."/> + help="up to the Nth nucleotide starting from the 5prime end. -1 means do not filter, 0 means check along the entire read, + 10 would make filter reads that are unique over the first 10 nucleotides."/> <param argument="-uniq_start" truevalue="-uniq_start" type="boolean" falsevalue="" label="Remove reads that start at the same position" @@ -90,17 +104,14 @@ help="Indels always counts as 1 regardless of length. Requires NM tag to be set."/> <param argument="-nosecondary" truevalue="-nosecondary" type="boolean" falsevalue="" - label="Remove reads that have the 0x100 flag set" - help="" /> - <param argument="-nosecondary" truevalue="-nosecondary" type="boolean" falsevalue="" - label="Remove reads that have the 0x100 flag set" - help="" /> + label="Remove secondary alignment reads" + help="Remove reads flagged with 0x100" /> <param argument="-noqcfail" truevalue="-noqcfail" type="boolean" falsevalue="" - label="Remove reads that have the 0x200 flag set" - help="" /> + label="Remove reads that do not pass the quality control" + help="Remove reads flagged with 0x200" /> <param argument="-nopcrdup" truevalue="-nopcrdup" type="boolean" falsevalue="" - label="Remove reads that have the 0x400 flag set" - help="" /> + label="Remove reads that are marked as PCR dupicates " + help="Remove reads flagged with 0x400" /> <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" /> @@ -142,13 +153,21 @@ <param name="nopcrdup" value="True"/> <output name="outfile" file="ngsutils_bam_filter_result3.bam" ftype="bam" /> </test> + <test> + <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> + <output name="outfile" file="ngsutils_bam_filter_input1.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" /> + </test> </tests> <help><![CDATA[ -Removes reads from a BAM file based on criteria +Removes reads from a BAM file based on criteria. -Given a BAM file, this script will only allow reads that meet filtering -criteria to be written to output. The output is another BAM file with the -reads not matching the criteria removed. +Given a BAM file, this tool will discard reads that did not meet the selected filtering criteria +The output is another BAM file with the reads not matching the criteria removed. Note: this does not adjust tag values reflecting any filtering. (for example: if a read mapped to two locations (IH:i:2), and one was removed by @@ -172,7 +191,7 @@ +--------------------------------+-------------------------------------------------+ | -noproperpair | Keep only not-properly paired reads | +--------------------------------+-------------------------------------------------+ -| -mask bitmask | Remove reads that match the mask (base 10/hex) | +| -mask bitmask | Remove reads that match the mask (e.g. 0x400) | +--------------------------------+-------------------------------------------------+ | -uniq {length} | Remove reads that are have the same sequence | | | Note: BAM file should be sorted |
--- a/macros.xml Tue Nov 10 15:08:52 2015 -0500 +++ b/macros.xml Wed Nov 11 13:03:30 2015 -0500 @@ -2,6 +2,7 @@ <token name="@WRAPPER_VERSION@">0.5.7</token> <xml name="requirements"> <requirements> + <requirement type="package" version="0.7.7">pysam</requirement> </requirements> </xml> <xml name="version">