Mercurial > repos > bgruening > deeptools
diff bamCoverage.xml @ 1:21d563d5f2b2 draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 05 Aug 2013 10:09:51 -0400 |
| parents | 09b65c12a75a |
| children | 1f312af2f8db |
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--- a/bamCoverage.xml Sat Aug 03 13:42:12 2013 -0400 +++ b/bamCoverage.xml Mon Aug 05 10:09:51 2013 -0400 @@ -1,11 +1,16 @@ <tool id="bamCoverage" name="bamCoverage" version="1.0"> <description>Given a BAM file, generates a coverage bigwig file. Multiple options available to count reads and normalize coverage.</description> <requirements> - <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement> + <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement> <requirement type="package" version="0.1">ucsc_tools</requirement> <requirement type="package" version="1.7.1">numpy</requirement> </requirements> - <command>bamCoverage + <command> + bamCoverage + + ##ToDo + --numberOfProcessors 4 + --bam '$bamInput' --bamIndex ${bamInput.metadata.bam_index} --outFileName '$outFileName' @@ -13,7 +18,6 @@ --fragmentLength $fragmentLength --binSize $binSize - #if $scaling.type=='rpkm': --normalizeUsingRPKM @@ -27,19 +31,18 @@ #if $advancedOpt.smoothLength: --smoothLength '$advancedOpt.smoothLength' #end if - + #if str($advancedOpt.region.value) != '': --region '$advancedOpt.region' #end if $advancedOpt.doNotExtendPairedEnds $advancedOpt.ignoreDuplicates - + #if $advancedOpt.minMappingQuality: --minMappingQuality '$advancedOpt.minMappingQuality' #end if - + #end if - --numberOfProcessors 4 </command> <inputs> @@ -64,59 +67,56 @@ <when value="rpkm"/> <when value="no"/> <when value="1x"> - <param name="normalizeTo1x" type="integer" value="2150570000" + <param name="normalizeTo1x" type="integer" value="2150570000" label="Genome size" help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/> </when> <when value="own"> - <param name="scaleFactor" type="float" value="1" size="3" + <param name="scaleFactor" type="float" value="1" size="3" label="Scale factor to multiply all values" /> - </when> + </when> </conditional> <param name="outFileFormat" type="select" label="Coverage file format"> <option value="bigwig" selected="true">bigwig</option> - <option value="bedgraph">bedgraph</option> + <option value="bedgraph">bedgraph</option> </param> - - + <conditional name="advancedOpt"> - <param name="showAdvancedOpt" type="select" label="Show advanced options" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> + <param name="showAdvancedOpt" type="select" label="Show advanced options" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> <when value="no" /> <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="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="region" type="text" value="" + label="Region of the genome to limit the operation to" + help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> - <param name="region" type="text" value="" - label="Region of the genome to limit the operation to" - help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> - - <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."/> - - <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"/> - </when> - </conditional> + <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."/> + <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"/> + </when> + </conditional> </inputs> <outputs> <data format="bigwig" name="outFileName"> - <change_format> - <when input="outFileFormat" value="bigwig" format="bigwig" /> - <when input="outFileFormat" value="bedgraph" format="bedgraph" /> - </change_format> + <change_format> + <when input="outFileFormat" value="bigwig" format="bigwig" /> + <when input="outFileFormat" value="bedgraph" format="bedgraph" /> + </change_format> </data> </outputs> <help> @@ -139,5 +139,4 @@ .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de </help> - </tool>