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annotate read_NVC.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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1 <tool id="rseqc_read_NVC" name="Read NVC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>to check the nucleotide composition bias</description>
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3 <macros>
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4 <import>rseqc_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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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 @BAM_SAM_INPUTS@
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16 read_NVC.py
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17 --input-file 'input.${extension}'
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18 --out-prefix output
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19 ${nx}
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20 --mapq ${mapq}
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21 ]]>
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22 </command>
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24 <inputs>
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25 <expand macro="bam_sam_param" />
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26 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
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27 <expand macro="mapq_param" />
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28 <expand macro="rscript_output_param" />
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29 </inputs>
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31 <outputs>
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32 <expand macro="pdf_output_data" filename="output.NVC_plot.pdf" />
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33 <expand macro="xls_output_data" filename="output.NVC.xls" />
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34 <expand macro="rscript_output_data" filename="output.NVC_plot.r" />
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35 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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40 <param name="rscript_output" value="true" />
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41 <output name="outputxls" file="output.NVC.xls" ftype="tabular"/>
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42 <output name="outputr" file="output.NVC_plot_r" />
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43 <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" />
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44 </test>
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45 </tests>
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46
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47 <help><![CDATA[
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48 read_NVC.py
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49 +++++++++++
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51 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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52 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
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53 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
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54 reads together, then calculating nucleotide composition for each position of read
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55 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
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56 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
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58 NOTE: this program expect a fixed read length
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60 Inputs
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61 ++++++++++++++
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63 Input BAM/SAM file
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64 Alignment file in BAM/SAM format.
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66 Include N,X in NVC plot
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67 Plots N and X alongside A, T, C, and G in plot.
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69 Output
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70 ++++++++++++++
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72 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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75 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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76 2. output.NVC_plot.r: R script to generate NVC plot.
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77 3. output.NVC_plot.pdf: NVC plot.
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79
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80 .. image:: $PATH_TO_IMAGES/NVC_plot.png
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81 :height: 600 px
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82 :width: 600 px
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83 :scale: 80 %
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85 @ABOUT@
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86
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87 ]]>
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88 </help>
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90 <expand macro="citations" />
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91
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92 </tool>