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annotate read_NVC.xml @ 7:d06c7d4fdc29 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit a63ead9b3f0c781032beabf8bed2c65445500291
author iuc
date Tue, 18 Sep 2018 05:21:29 -0400
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children d7f6b3653d84
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1 <tool id="rseqc_read_NVC" name="Read NVC" version="@WRAPPER_VERSION@">
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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 <expand macro="requirements" />
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[read_NVC.py --version]]></version_command>
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14 <command><![CDATA[
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15 read_NVC.py
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16 --input-file '${input}'
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17 --out-prefix output
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18 ${nx}
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19 --mapq ${mapq}
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20 ]]>
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21 </command>
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23 <inputs>
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24 <expand macro="bam_sam_param" />
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25 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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26 <expand macro="mapq_param" />
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27 <expand macro="rscript_output_param" />
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28 </inputs>
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30 <outputs>
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31 <expand macro="pdf_output_data" filename="output.NVC_plot.pdf" />
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32 <expand macro="xls_output_data" filename="output.NVC.xls" />
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33 <expand macro="rscript_output_data" filename="output.NVC_plot.r" />
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34 </outputs>
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35
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36 <tests>
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37 <test>
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38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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39 <param name="rscript_output" value="true" />
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40 <output name="outputxls" file="output.NVC.xls" />
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41 <output name="outputr" file="output.NVC_plot.r" />
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42 <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" />
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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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50 This module is used to check the nucleotide composition bias. Due to random priming, certain
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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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
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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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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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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78
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79 .. image:: $PATH_TO_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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83
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84 @ABOUT@
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85
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86 ]]>
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87 </help>
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89 <expand macro="citations" />
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90
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91 </tool>