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annotate geneBody_coverage2.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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1 <tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>read coverage over gene body</description>
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3 <expand macro="bio_tools"/>
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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[geneBody_coverage2.py --version]]></version_command>
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14 <command><![CDATA[
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15 geneBody_coverage2.py -i '${input}' -r '${refgene}' -o output
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16 ]]>
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17 </command>
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18
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19 <inputs>
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20 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
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21 <expand macro="refgene_param" />
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22 <expand macro="rscript_output_param" />
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23 </inputs>
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24
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25 <outputs>
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26 <expand macro="pdf_output_data" filename="output.geneBodyCoverage.pdf" />
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27 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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28 <expand macro="rscript_output_data" filename="output.geneBodyCoverage_plot.r" />
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29 </outputs>
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31 <tests>
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32 <test expect_num_outputs="3">
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33 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig" />
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34 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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35 <param name="rscript_output" value="true" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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36 <output name="outputpdf" file="output.geneBodyCoverage2.curves.pdf" compare="sim_size" />
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37 <output name="outputr" file="output.geneBodyCoverage2_r" />
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38 <output name="outputtxt" file="output.geneBodyCoverage2.txt" />
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39 </test>
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40 </tests>
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42 <help><![CDATA[
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43 geneBody_coverage2.py
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44 +++++++++++++++++++++
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45
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46 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
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47 requires much less memory. The BigWig file could be arbitrarily large.
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50 Inputs
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51 ++++++++++++++
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52
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53 Input BAM/SAM file
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54 Alignment file in BAM/SAM format.
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55
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56 Reference gene model
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57 Gene Model in BED format.
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60 Outputs
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61 ++++++++++++++
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62
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63 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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64
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65 Example output:
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66 .. image:: $PATH_TO_IMAGES/geneBody_coverage.png
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67 :height: 600 px
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68 :width: 600 px
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69 :scale: 80 %
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71 @ABOUT@
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72
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73 ]]>
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74 </help>
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75
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76 <expand macro="citations" />
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77
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78 </tool>