Mercurial > repos > iuc > bedtools
diff multiCov.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
---|---|
date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | 3e38c9b3214f |
line wrap: on
line diff
--- a/multiCov.xml Mon Dec 17 14:23:31 2018 -0500 +++ b/multiCov.xml Mon Apr 29 05:55:48 2019 -0400 @@ -1,75 +1,70 @@ -<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@WRAPPER_VERSION@"> +<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@"> <description>counts coverage from multiple BAMs at specific intervals</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> - <command> -<![CDATA[ - #for $i, $bam in enumerate( $bams ): - ln -s -f $bam ${i}.bam && - ln -s -f $bam.metadata.bam_index ${i}.bam.bai && - #end for + <command><![CDATA[ +#for $i, $bam in enumerate($bams): + ln -s -f '$bam' ${i}.bam && + ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai && +#end for - bedtools multicov - -bed '$input' - -bams - #for $i, $bam in enumerate( $bams ): - '${i}.bam' - #end for - $strand - -f $overlap - $reciprocal - $split - -q $q - $duplicate - $failed - $proper - > '$output' -]]> - </command> +bedtools multicov +-bed '$input' +-bams +#for $i, $bam in enumerate($bams): + '${i}.bam' +#end for +$strand +@OVERLAP@ +$reciprocal +$split +-q $q +$duplicate +$failed +$proper +> '$output' + ]]></command> <inputs> - <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" /> + <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" /> <!-- Additional files, if the user needs more --> - <param name="bams" format="bam" type="data" multiple="True" label="BAM file" /> + <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" /> <expand macro="strand2" /> <expand macro="overlap" /> <expand macro="reciprocal" /> <expand macro="split" /> - <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" /> - <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue="" + <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" /> + <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false" label="Include duplicate reads" - help="Default counts non-duplicates only. (-D)" /> - <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" + help="Default counts non-duplicates only" /> + <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false" label="Include failed-QC reads" - help="Default counts pass-QC reads only (-F)"/> - <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" + help="Default counts pass-QC reads only"/> + <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Only count proper pairs" - help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" /> + help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" /> </inputs> <outputs> - <data name="output" metadata_source="input" format_source="input" /> + <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> <test> <param name="input" value="multiCov1.bed" ftype="bed" /> <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> <param name="q" value="1"/> - <param name="split" value="False"/> + <param name="split" value=""/> <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ **What it does** bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file. - @REFERENCES@ -]]> - </help> + ]]></help> <expand macro="citations" /> </tool>