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annotate read_NVC.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
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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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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <version_command><![CDATA[read_NVC.py --version]]></version_command>
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10 <command><![CDATA[
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11 @BAM_SAM_INPUTS@
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12 read_NVC.py
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13 --input-file 'input.${extension}'
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14 --out-prefix output
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15 ${nx}
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16 --mapq ${mapq}
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro="bam_sam_param"/>
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21 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
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22 <expand macro="mapq_param"/>
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23 <expand macro="rscript_output_param"/>
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24 </inputs>
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25 <outputs>
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26 <expand macro="pdf_output_data" filename="output.NVC_plot.pdf"/>
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27 <expand macro="xls_output_data" filename="output.NVC.xls"/>
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28 <expand macro="rscript_output_data" filename="output.NVC_plot.r"/>
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29 </outputs>
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30 <tests>
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31 <test expect_num_outputs="3">
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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32 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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33 <param name="rscript_output" value="true"/>
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34 <output name="outputxls" file="output.NVC.xls" ftype="tabular"/>
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35 <output name="outputr" file="output.NVC_plot_r"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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36 <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 read_NVC.py
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41 +++++++++++
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42
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43 This module is used to check the nucleotide composition bias. Due to random priming, certain
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44 patterns are over represented at the beginning (5'end) of reads. This bias could be easily
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45 examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all
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46 reads together, then calculating nucleotide composition for each position of read
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47 (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is
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48 randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
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50 NOTE: this program expect a fixed read length
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51
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52 Inputs
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53 ++++++++++++++
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54
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55 Input BAM/SAM file
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56 Alignment file in BAM/SAM format.
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57
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58 Include N,X in NVC plot
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59 Plots N and X alongside A, T, C, and G in plot.
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61 Output
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62 ++++++++++++++
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64 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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65
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67 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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68 2. output.NVC_plot.r: R script to generate NVC plot.
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69 3. output.NVC_plot.pdf: NVC plot.
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72 .. image:: $PATH_TO_IMAGES/NVC_plot.png
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73 :height: 600 px
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74 :width: 600 px
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75 :scale: 80 %
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77 @ABOUT@
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78
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79 ]]>
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80 </help>
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81 <expand macro="citations"/>
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82 </tool>