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comparison read_duplication.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
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62:473382134e56 63:27e16a30667a
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> 2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
3 <macros> 3 <macros>
4 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7
8 <expand macro="requirements" /> 7 <expand macro="requirements" />
9
10 <expand macro="stdio" /> 8 <expand macro="stdio" />
11
12 <version_command><![CDATA[read_duplication.py --version]]></version_command> 9 <version_command><![CDATA[read_duplication.py --version]]></version_command>
13
14 <command><![CDATA[ 10 <command><![CDATA[
15 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
16 read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq} 12 read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
17 ]]> 13 ]]>
18 </command> 14 </command>
19
20 <inputs> 15 <inputs>
21 <expand macro="bam_sam_param" /> 16 <expand macro="bam_sam_param" />
22 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/> 17 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
23 <expand macro="mapq_param" /> 18 <expand macro="mapq_param" />
24 <expand macro="rscript_output_param" /> 19 <expand macro="rscript_output_param" />
25 </inputs> 20 </inputs>
26
27 <outputs> 21 <outputs>
28 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> 22 <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
29 <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/> 23 <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/>
30 <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/> 24 <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/>
31 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/> 25 <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
32 </outputs> 26 </outputs>
33
34 <tests> 27 <tests>
35 <test> 28 <test expect_num_outputs="4">
36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 29 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
37 <param name="rscript_output" value="true" /> 30 <param name="rscript_output" value="true" />
38 <output name="outputxls" file="output.pos.DupRate.xls" ftype="tabular"/> 31 <output name="outputxls" file="output.pos.DupRate.xls" ftype="tabular"/>
39 <output name="outputseqxls" file="output.seq.DupRate.xls" ftype="tabular"/> 32 <output name="outputseqxls" file="output.seq.DupRate.xls" ftype="tabular"/>
40 <output name="outputr" file="output.DupRate_plot_r" /> 33 <output name="outputr" file="output.DupRate_plot_r" />
41 <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" /> 34 <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" />
42 </test> 35 </test>
43 </tests> 36 </tests>
44
45 <help><![CDATA[ 37 <help><![CDATA[
46 read_duplication.py 38 read_duplication.py
47 +++++++++++++++++++ 39 +++++++++++++++++++
48 40
49 Two strategies were used to determine reads duplication rate: 41 Two strategies were used to determine reads duplication rate:
75 67
76 @ABOUT@ 68 @ABOUT@
77 69
78 ]]> 70 ]]>
79 </help> 71 </help>
80
81 <expand macro="citations" /> 72 <expand macro="citations" />
82
83 </tool> 73 </tool>