Mercurial > repos > nilesh > rseqc
comparison read_duplication.xml @ 63:27e16a30667a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author | iuc |
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date | Tue, 09 Apr 2024 11:24:55 +0000 |
parents | 473382134e56 |
children |
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62:473382134e56 | 63:27e16a30667a |
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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> |