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annotate geneBody_coverage2.xml @ 3:71ed55a3515a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:22:57 -0400
parents f92b87abef3d
children 017eaaf58e5e
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71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="@WRAPPER_VERSION@">
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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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 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[geneBody_coverage2.py --version]]></version_command>
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16 <command><![CDATA[
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17 geneBody_coverage2.py -i '${input}' -r '${refgene}' -o output
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18 ]]>
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19 </command>
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21 <inputs>
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22 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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23 <expand macro="refgene_param" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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24 </inputs>
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26 <outputs>
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27 <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" />
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28 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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29 <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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30 </outputs>
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31
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32 <tests>
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33 <test>
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34 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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35 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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36 <param name="rscript_output" value="true" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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37 <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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38 <output name="outputr" file="output.geneBodyCoverage2.r" />
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39 <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
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40 </test>
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41 </tests>
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42
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43 <help><![CDATA[
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44 geneBody_coverage2.py
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45 +++++++++++++++++++++
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47 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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48 requires much less memory. The BigWig file could be arbitrarily large.
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51 Inputs
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52 ++++++++++++++
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53
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54 Input BAM/SAM file
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55 Alignment file in BAM/SAM format.
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57 Reference gene model
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58 Gene Model in BED format.
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61 Outputs
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62 ++++++++++++++
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63
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64 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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65
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66 Example output:
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67 .. image:: $PATH_TO_IMAGES/geneBody_coverage.png
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68 :height: 600 px
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69 :width: 600 px
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70 :scale: 80 %
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71
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72 @ABOUT@
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74 ]]>
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75 </help>
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76
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77 <expand macro="citations" />
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79 </tool>