Mercurial > repos > bgruening > deeptools
diff bamCoverage.xml @ 30:5231f398d784 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
| author | bgruening |
|---|---|
| date | Tue, 20 Oct 2015 14:43:12 -0400 |
| parents | 3a2aab18a217 |
| children |
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--- a/bamCoverage.xml Tue Sep 16 13:46:05 2014 -0400 +++ b/bamCoverage.xml Tue Oct 20 14:43:12 2015 -0400 @@ -1,68 +1,71 @@ <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0"> <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">bamCoverage</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> +<![CDATA[ bamCoverage - @THREADS@ + @THREADS@ - --bam '$bamInput' - --bamIndex ${bamInput.metadata.bam_index} - --outFileName '$outFileName' - --outFileFormat '$outFileFormat' + --bam '$bamInput' + --bamIndex ${bamInput.metadata.bam_index} + --outFileName '$outFileName' + --outFileFormat '$outFileFormat' - --fragmentLength $fragmentLength - --binSize $binSize + --fragmentLength $fragmentLength + --binSize $binSize - #if $scaling.type=='rpkm': - --normalizeUsingRPKM - #elif $scaling.type=='1x': - #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize - #else: - --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt - #end if - #elif $scaling.type=='own': - --scaleFactor $scaling.scaleFactor - #end if - - #if str($region).strip() != '': - --region '$region' - #end if - - #if $advancedOpt.showAdvancedOpt == "yes": - #if $advancedOpt.smoothLength: - --smoothLength '$advancedOpt.smoothLength' + #if $scaling.type=='rpkm': + --normalizeUsingRPKM + #elif $scaling.type=='1x': + #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize + #else: + --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt + #end if + #elif $scaling.type=='own': + --scaleFactor $scaling.scaleFactor #end if - $advancedOpt.doNotExtendPairedEnds - $advancedOpt.ignoreDuplicates - - #if $advancedOpt.minMappingQuality: - --minMappingQuality '$advancedOpt.minMappingQuality' + #if str($region).strip() != '': + --region '$region' #end if - --missingDataAsZero $advancedOpt.missingDataAsZero + #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.smoothLength: + --smoothLength '$advancedOpt.smoothLength' + #end if + + $advancedOpt.doNotExtendPairedEnds + $advancedOpt.ignoreDuplicates - ##if str($advancedOpt.ignoreForNormalization).strip() != '': - ## --ignoreForNormalization $advancedOpt.ignoreForNormalization - ##end if + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + + --missingDataAsZero $advancedOpt.missingDataAsZero - #end if + ##if str($advancedOpt.ignoreForNormalization).strip() != '': + ## --ignoreForNormalization $advancedOpt.ignoreForNormalization + ##end if + #if $samFlag: + --samFlag $samFlag + #end if + #end if +]]> </command> <inputs> <param name="bamInput" format="bam" type="data" label="BAM file" help="The BAM file must be sorted."/> - <param name="fragmentLength" type="integer" value="300" min="1" + <param name="fragmentLength" type="integer" value="200" min="1" label="Length of the average fragment size" - help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> + help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length. (--fragmentLength)"/> <param name="binSize" type="integer" value="50" min="1" label="Bin size in bp" @@ -102,22 +105,13 @@ <when value="yes"> <param name="smoothLength" type="integer" value="1" optional="true" min="1" label="Smooth values using the following length (in bp)" - help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> - - <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" - label="Do not extend paired ends" - help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> + help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied. (--smoothLength)"/> - <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" - label="Ignore duplicates" - help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> - - <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" - label="Minimum mapping quality" - help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> - + <expand macro="doNotExtendPairedEnds" /> + <expand macro="ignoreDuplicates" /> + <expand macro="minMappingQuality" /> <expand macro="missingDataAsZero" /> - + <expand macro="samFlag" /> <!-- <param name="ignoreForNormalization" type="text" value="" size="50" label="regions that should be excluded for calculating the scaling factor" help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" /> @@ -133,8 +127,46 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <param name="type" value="no" /> + <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" /> + </test> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" /> + </test> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" /> + </test> + <test> + <param name="bamInput" value="phiX.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" /> + </test> + <test> + <param name="bamInput" value="phiX.bam" ftype="bam" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or @@ -160,7 +192,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>