Mercurial > repos > iuc > ngsutils_bam_filter
changeset 1:8187a729d9f4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
| author | iuc |
|---|---|
| date | Sun, 06 Dec 2015 05:03:12 -0500 |
| parents | 4e4e4093d65d |
| children | 7a68005de299 |
| files | bam_filter.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/exclude.bed test-data/ngsutils_bam_filter_input4.bam test-data/ngsutils_bam_filter_result5.bam test-data/ngsutils_bam_filter_result6.bam |
| diffstat | 11 files changed, 19 insertions(+), 10 deletions(-) [+] |
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--- 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[