Mercurial > repos > lparsons > rseqc

annotate read_NVC.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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1 <tool id="rseqc_read_NVC" name="Read NVC" version="2.4galaxy1">
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2 <description>to check the nucleotide composition bias</description>
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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <expand macro="requirement_package_r" />
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10 <expand macro="requirement_package_numpy" />
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11 <expand macro="requirement_package_rseqc" />
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12 </requirements>
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14 <expand macro="stdio" />
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16 <version_command><![CDATA[read_NVC.py --version]]></version_command>
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18 <command>
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19 read_NVC.py
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20 --input-file $input
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21 --out-prefix output
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22 $nx
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23 --mapq $mapq
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24 </command>
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26 <inputs>
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27 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
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28 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
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29 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
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30 </inputs>
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32 <outputs>
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33 <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
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34 <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
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35 <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
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36 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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41 <output name="outputxls" file="output.NVC.xls"/>
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42 <output name="outputr" file="output.NVC_plot.r"/>
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43 </test>
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44 </tests>
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46 <help><![CDATA[
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47 read_NVC.py
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48 +++++++++++
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49
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50 This module is used to check the nucleotide composition bias. Due to random priming, certain
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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51 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
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52 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
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53 reads together, then calculating nucleotide composition for each position of read
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54 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
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55 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
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56
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57 NOTE: this program expect a fixed read length
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58
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59 Inputs
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60 ++++++++++++++
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61
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62 Input BAM/SAM file
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63 Alignment file in BAM/SAM format.
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64
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65 Include N,X in NVC plot
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66 Plots N and X alongside A, T, C, and G in plot.
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67
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68 Output
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69 ++++++++++++++
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70
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71 This module is used to check the nucleotide composition bias. Due to random priming, certain patterns are over represented at the beginning (5'end) of reads. This bias could be easily examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all reads together, then calculating nucleotide composition for each position of read (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
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74 1. output.NVC.xls: plain text file, each row is position of read (or sequencing cycle), each column is nucleotide (A,C,G,T,N,X)
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75 2. output.NVC_plot.r: R script to generate NVC plot.
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76 3. output.NVC_plot.pdf: NVC plot.
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79 .. image:: http://rseqc.sourceforge.net/_images/NVC_plot.png
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80 :height: 600 px
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81 :width: 600 px
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82 :scale: 80 %
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84 -----
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86 About RSeQC
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87 +++++++++++
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89 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
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91 The RSeQC package is licensed under the GNU GPL v3 license.
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93 .. image:: http://rseqc.sourceforge.net/_static/logo.png
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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94
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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95 .. _RSeQC: http://rseqc.sourceforge.net/
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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96 ]]>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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97 </help>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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98
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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99 <expand macro="citations" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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100
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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101 </tool>