Mercurial > repos > lparsons > rseqc

annotate geneBody_coverage2.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
parents 306127635959
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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_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="2.4galaxy1">
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2 <description>
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3 Read coverage over gene body
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4 </description>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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10 <requirements>
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11 <expand macro="requirement_package_r" />
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12 <expand macro="requirement_package_numpy" />
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13 <expand macro="requirement_package_rseqc" />
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14 </requirements>
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16 <expand macro="stdio" />
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18 <version_command><![CDATA[geneBody_coverage2.py --version]]></version_command>
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20 <command><![CDATA[
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21 geneBody_coverage2.py -i $input -r $refgene -o output
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22 ]]>
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23 </command>
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25 <inputs>
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26 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
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27 <param name="refgene" type="data" label="Reference Genome" format="bed" />
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28 </inputs>
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30 <outputs>
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31 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
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32 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
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33 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
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34 </outputs>
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36 <!-- Unable to succefully run this script, it seems deprecated and should probably be dropped
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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.bigwig"/>
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40 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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41 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/>
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42 <output name="outputr" file="output.geneBodyCoverage.r"/>
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43 <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
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44 </test>
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45 </tests>
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46 -->
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48 <help><![CDATA[
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49 geneBody_coverage2.py
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50 +++++++++++++++++++++
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51
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52 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
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53 requires much less memory. The BigWig file could be arbitrarily large.
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56 Inputs
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57 ++++++++++++++
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59 Input BAM/SAM file
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60 Alignment file in BAM/SAM format.
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62 Reference gene model
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63 Gene Model in BED format.
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66 Outputs
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67 ++++++++++++++
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69 Read coverage over gene body. This module is used to check if reads coverage is uniform and if there is any 5’/3’ bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates a plot illustrating the coverage profile along the gene body. NOTE: this module requires lots of memory for large BAM files, because it load the entire BAM file into memory. We add another script "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input. It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
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71 Example output:
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72 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/geneBody_coverage.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 -----
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79 About RSeQC
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80 +++++++++++
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82 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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84 The RSeQC package is licensed under the GNU GPL v3 license.
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86 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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88 .. _RSeQC: http://rseqc.sourceforge.net/
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90 ]]>
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91 </help>
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93 <expand macro="citations" />
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 </tool>