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comparison read_NVC.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>to check the nucleotide composition bias</description> 2 <description>to check the nucleotide composition bias</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 7 <expand macro="requirements"/>
8 <expand macro="requirements" /> 8 <expand macro="stdio"/>
9
10 <expand macro="stdio" />
11
12 <version_command><![CDATA[read_NVC.py --version]]></version_command> 9 <version_command><![CDATA[read_NVC.py --version]]></version_command>
13
14 <command><![CDATA[ 10 <command><![CDATA[
15 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
16 read_NVC.py 12 read_NVC.py
17 --input-file 'input.${extension}' 13 --input-file 'input.${extension}'
18 --out-prefix output 14 --out-prefix output
19 ${nx} 15 ${nx}
20 --mapq ${mapq} 16 --mapq ${mapq}
21 ]]> 17 ]]>
22 </command> 18 </command>
23
24 <inputs> 19 <inputs>
25 <expand macro="bam_sam_param" /> 20 <expand macro="bam_sam_param"/>
26 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/> 21 <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/>
27 <expand macro="mapq_param" /> 22 <expand macro="mapq_param"/>
28 <expand macro="rscript_output_param" /> 23 <expand macro="rscript_output_param"/>
29 </inputs> 24 </inputs>
30
31 <outputs> 25 <outputs>
32 <expand macro="pdf_output_data" filename="output.NVC_plot.pdf" /> 26 <expand macro="pdf_output_data" filename="output.NVC_plot.pdf"/>
33 <expand macro="xls_output_data" filename="output.NVC.xls" /> 27 <expand macro="xls_output_data" filename="output.NVC.xls"/>
34 <expand macro="rscript_output_data" filename="output.NVC_plot.r" /> 28 <expand macro="rscript_output_data" filename="output.NVC_plot.r"/>
35 </outputs> 29 </outputs>
36
37 <tests> 30 <tests>
38 <test> 31 <test expect_num_outputs="3">
39 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 32 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
40 <param name="rscript_output" value="true" /> 33 <param name="rscript_output" value="true"/>
41 <output name="outputxls" file="output.NVC.xls" ftype="tabular"/> 34 <output name="outputxls" file="output.NVC.xls" ftype="tabular"/>
42 <output name="outputr" file="output.NVC_plot_r" /> 35 <output name="outputr" file="output.NVC_plot_r"/>
43 <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" /> 36 <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size"/>
44 </test> 37 </test>
45 </tests> 38 </tests>
46
47 <help><![CDATA[ 39 <help><![CDATA[
48 read_NVC.py 40 read_NVC.py
49 +++++++++++ 41 +++++++++++
50 42
51 This module is used to check the nucleotide composition bias. Due to random priming, certain 43 This module is used to check the nucleotide composition bias. Due to random priming, certain
84 76
85 @ABOUT@ 77 @ABOUT@
86 78
87 ]]> 79 ]]>
88 </help> 80 </help>
89 81 <expand macro="citations"/>
90 <expand macro="citations" />
91
92 </tool> 82 </tool>