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annotate read_duplication.xml @ 61:5968573462fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:23:05 +0000
parents 1421603cc95b
children 473382134e56
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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 <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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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@
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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16 read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
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17 ]]>
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18 </command>
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19
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20 <inputs>
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21 <expand macro="bam_sam_param" />
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22 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
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23 <expand macro="mapq_param" />
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24 <expand macro="rscript_output_param" />
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25 </inputs>
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26
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27 <outputs>
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28 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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29 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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30 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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31 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
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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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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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40 <output name="outputr" file="output.DupRate_plot_r" />
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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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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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59
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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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78 ]]>
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79 </help>
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81 <expand macro="citations" />
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82
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83 </tool>