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annotate read_duplication.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_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</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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7
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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_duplication.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_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
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17 ]]>
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18 </command>
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19
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20 <inputs>
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21 <expand macro="bam_sam_param" />
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22 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
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23 <expand macro="mapq_param" />
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24 <expand macro="rscript_output_param" />
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25 </inputs>
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26
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27 <outputs>
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28 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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29 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position xls)"/>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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30 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence xls)"/>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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31 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" />
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32 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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37 <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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38 <output name="outputxls" file="output.pos.DupRate.xls" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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39 <output name="outputseqxls" file="output.seq.DupRate.xls" />
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40 <output name="outputr" file="output.DupRate_plot_r" />
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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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41 <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
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42 </test>
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43 </tests>
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45 <help><![CDATA[
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46 read_duplication.py
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47 +++++++++++++++++++
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48
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49 Two strategies were used to determine reads duplication rate:
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50
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51 * Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
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52 * Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads.
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54 Inputs
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55 ++++++++++++++
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56
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57 Input BAM/SAM file
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58 Alignment file in BAM/SAM format.
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60 Upper Limit of Plotted Duplicated Times (default=500)
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61 Only used for plotting.
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62
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63 Output
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64 ++++++++++++++
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65
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66 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
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67 2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
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68 3. output.DupRate_plot.r: R script to generate pdf file
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69 4. output.DupRate_plot.pdf: graphical output generated from R script
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71 .. image:: $PATH_TO_IMAGES/duplicate.png
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72 :height: 600 px
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73 :width: 600 px
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74 :scale: 80 %
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76 @ABOUT@
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77
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78 ]]>
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79 </help>
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80
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81 <expand macro="citations" />
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82
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83 </tool>