Mercurial > repos > nilesh > rseqc
view deletion_profile.xml @ 54:5873cd7afb67 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82
author | iuc |
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date | Wed, 13 Jun 2018 18:02:25 -0400 |
parents | 09846d5169fa |
children | dbedfc5f5a3c |
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<tool id="rseqc_deletion_profile" name="Deletion Profile" version="@WRAPPER_VERSION@"> <description> calculates the distributions of deleted nucleotides across reads </description> <macros> <import>rseqc_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <version_command><![CDATA[deletion_profile.py --version]]></version_command> <command><![CDATA[ deletion_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq} ]]> </command> <inputs> <expand macro="bam_param" /> <expand macro="readlength_param" /> <expand macro="readnum_param" /> <expand macro="mapq_param" /> <expand macro="rscript_output_param" /> </inputs> <outputs> <expand macro="pdf_output_data" filename="output.deletion_profile.pdf" /> <expand macro="xls_output_data" filename="output.deletion_profile.txt" /> <expand macro="rscript_output_data" filename="output.deletion_profile.r" /> </outputs> <tests> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="readlength" value="101" /> <param name="rscript_output" value="true" /> <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" /> <output name="outputxls" file="output.deletion_profile.txt" /> <output name="outputr" file="output.deletion_profile.r" /> </test> </tests> <help><![CDATA[ deletion_profile.py +++++++++++++++++++ Calculate the distributions of deleted nucleotides across reads. Inputs ++++++ Input BAM/SAM file Alignment file in BAM/SAM format. Alignment length of read It is usually set to the orignial read length. For example, all these cigar strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment length is 101. [required] Number of aligned reads used Number of aligned reads with deletions used to calculate the deletion profile. default=1000000 Minimum mapping quality Minimum mapping quality for an alignment to be considered as "uniquely mapped". default=30 Sample Output ++++++++++++++ .. image:: $PATH_TO_IMAGES/out.deletion_profile.png :height: 600 px :width: 600 px :scale: 80 % @ABOUT@ ]]> </help> <expand macro="citations" /> </tool>