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comparison clipping_profile.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
3 estimates clipping profile of RNA-seq reads from BAM or SAM file 3 estimates clipping profile of RNA-seq reads from BAM or SAM file
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>rseqc_macros.xml</import> 6 <import>rseqc_macros.xml</import>
7 </macros> 7 </macros>
8
9 <expand macro="bio_tools"/> 8 <expand macro="bio_tools"/>
10 9 <expand macro="requirements"/>
11 <expand macro="requirements" /> 10 <expand macro="stdio"/>
12
13 <expand macro="stdio" />
14
15 <version_command><![CDATA[clipping_profile.py --version]]></version_command> 11 <version_command><![CDATA[clipping_profile.py --version]]></version_command>
16
17 <command><![CDATA[ 12 <command><![CDATA[
18 @BAM_SAM_INPUTS@ 13 @BAM_SAM_INPUTS@
19 clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}" 14 clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
20 ]]> 15 ]]>
21 </command> 16 </command>
22
23 <inputs> 17 <inputs>
24 <expand macro="bam_param" /> 18 <expand macro="bam_param"/>
25 <expand macro="mapq_param" /> 19 <expand macro="mapq_param"/>
26 <expand macro="layout_param" /> 20 <expand macro="layout_param"/>
27 <expand macro="rscript_output_param" /> 21 <expand macro="rscript_output_param"/>
28 </inputs> 22 </inputs>
29
30 <outputs> 23 <outputs>
31 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/> 24 <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/>
32 <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/> 25 <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/>
33 <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/> 26 <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/>
34 </outputs> 27 </outputs>
35
36 <tests> 28 <tests>
37 <test> 29 <test expect_num_outputs="2">
38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 30 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
39 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> 31 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/>
40 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> 32 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
41 </test> 33 </test>
42 <test> 34 <test expect_num_outputs="3">
43 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
44 <param name="rscript_output" value="true" /> 36 <param name="rscript_output" value="true"/>
45 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> 37 <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/>
46 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> 38 <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/>
47 <output name="outputr" file="output.clipping_profile_r" /> 39 <output name="outputr" file="output.clipping_profile_r"/>
48 </test> 40 </test>
49 </tests> 41 </tests>
50
51 <help><![CDATA[ 42 <help><![CDATA[
52 clipping_profile.py 43 clipping_profile.py
53 +++++++++++++++++++ 44 +++++++++++++++++++
54 45
55 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file. 46 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
79 70
80 @ABOUT@ 71 @ABOUT@
81 72
82 ]]> 73 ]]>
83 </help> 74 </help>
84 75 <expand macro="citations"/>
85 <expand macro="citations" />
86
87 </tool> 76 </tool>