Mercurial > repos > nilesh > rseqc
view bam2wig.xml @ 59:dbedfc5f5a3c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
author | iuc |
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date | Sat, 18 Dec 2021 19:41:19 +0000 |
parents | 080fd5739bb4 |
children | 1421603cc95b |
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<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@"> <description> converts all types of RNA-seq data from .bam to .wig </description> <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <version_command><![CDATA[bam2wig.py --version]]></version_command> <command><![CDATA[ ln -sf '${input}' 'input.bam' && ln -sf '${input.metadata.bam_index}' 'input.bam.bai' && bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile #if str($strand_type.strand_specific) == "pair" -d #if str($strand_type.pair_type) == "sd" '1++,1--,2+-,2-+' #else '1+-,1-+,2++,2--' #end if #end if #if str($strand_type.strand_specific) == "single" -d #if str($strand_type.single_type) == "s" '++,--' #else '+-,-+' #end if #end if #if str($wigsum_type.wigsum_type_selector) == "normalize": -t ${wigsum_type.totalwig} #end if @MULTIHITS@ ]]> </command> <inputs> <expand macro="bam_param" /> <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/> <expand macro="multihits_param" /> <conditional name="wigsum_type"> <param name="wigsum_type_selector" type="select" label="Normalization"> <option value="normalize">Normalize to specified sum</option> <option value="raw" selected="true">Do not normalize</option> </param> <when value="normalize"> <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/> </when> <when value="raw"/> </conditional> <expand macro="strand_type_param" /> </inputs> <outputs> <data format="wig" name="output" from_work_dir="outfile.wig"> <filter>strand_type['strand_specific'] == 'none'</filter> </data> <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)"> <filter>strand_type['strand_specific'] != 'none'</filter> </data> <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)"> <filter>strand_type['strand_specific'] != 'none'</filter> </data> </outputs> <tests> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <output name="output" file="testwig.wig"/> </test> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <param name="multihits_type_selector" value="skip_multihits"/> <param name="mapq" value="20"/> <output name="output" file="testwig.wig"/> </test> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <param name="strand_specific" value="pair"/> <param name="pair_type" value="sd"/> <output name="outputfwd" file="testwig.Forward.wig"/> <output name="outputrv" file="testwig.Reverse.wig"/> </test> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <param name="wigsum_type_selector" value="normalize"/> <param name="totalwig" value="100"/> <output name="output" file="testwig_wigsum100.wig"/> </test> </tests> <help><![CDATA[ bam2wig.py ++++++++++ Visualization is the most straightforward and effective way to QC your RNA-seq data. For example, change of expression or new splicing can be easily checked by visually comparing two RNA-seq tracks using genome browser such as UCSC_, IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_ format into wiggle_ format in one-stop. wiggle_ files can then be easily converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and it's particular useful to display large, continuous dataset on genome browser. Inputs ++++++++++++++ Input BAM file Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools. Chromosome size file Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file. Specified wigsum (default=none) Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization. Skip multiple Hit reads skips multiple hit reads or only use uniquely mapped reads Strand-specific (default=none) How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py Outputs ++++++++++++++ If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq is strand specific, two wig files corresponding to Forward and Reverse will be generated. @ABOUT@ .. _UCSC: http://genome.ucsc.edu/index.html .. _IGB: http://bioviz.org/igb/ .. _IGV: http://software.broadinstitute.org/software/igv/ .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 ]]> </help> <expand macro="citations" /> </tool>