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comparison mismatch_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
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 <expand macro="bio_tools"/> 8 <expand macro="bio_tools"/>
9 9 <expand macro="requirements"/>
10 <expand macro="requirements" /> 10 <expand macro="stdio"/>
11
12 <expand macro="stdio" />
13
14 <version_command><![CDATA[mismatch_profile.py --version]]></version_command> 11 <version_command><![CDATA[mismatch_profile.py --version]]></version_command>
15
16 <command><![CDATA[ 12 <command><![CDATA[
17 @BAM_SAM_INPUTS@ 13 @BAM_SAM_INPUTS@
18 mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq} 14 mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
19 ]]> 15 ]]>
20 </command> 16 </command>
21
22 <inputs> 17 <inputs>
23 <expand macro="bam_param" /> 18 <expand macro="bam_param"/>
24 <expand macro="readlength_param" /> 19 <expand macro="readlength_param"/>
25 <expand macro="readnum_param" /> 20 <expand macro="readnum_param"/>
26 <expand macro="mapq_param" /> 21 <expand macro="mapq_param"/>
27 <expand macro="rscript_output_param" /> 22 <expand macro="rscript_output_param"/>
28 </inputs> 23 </inputs>
29
30 <outputs> 24 <outputs>
31 <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf" /> 25 <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf"/>
32 <expand macro="xls_output_data" filename="output.mismatch_profile.xls" /> 26 <expand macro="xls_output_data" filename="output.mismatch_profile.xls"/>
33 <expand macro="rscript_output_data" filename="output.mismatch_profile.r" /> 27 <expand macro="rscript_output_data" filename="output.mismatch_profile.r"/>
34 </outputs> 28 </outputs>
35
36 <tests> 29 <tests>
37 <test> 30 <test expect_num_outputs="3">
38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 31 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
39 <param name="read_align_length" value="101" /> 32 <param name="read_align_length" value="101"/>
40 <param name="rscript_output" value="true" /> 33 <param name="rscript_output" value="true"/>
41 <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" /> 34 <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size"/>
42 <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/> 35 <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/>
43 <output name="outputr" file="output.mismatch_profile_r"/> 36 <output name="outputr" file="output.mismatch_profile_r"/>
44 </test> 37 </test>
45 </tests> 38 </tests>
46
47 <help><![CDATA[ 39 <help><![CDATA[
48 mismatch_profile.py 40 mismatch_profile.py
49 +++++++++++++++++++ 41 +++++++++++++++++++
50 42
51 Calculate the distribution of mismatches across reads. 43 Calculate the distribution of mismatches across reads.
82 @ABOUT@ 74 @ABOUT@
83 75
84 ]]> 76 ]]>
85 77
86 </help> 78 </help>
87 79 <expand macro="citations"/>
88 <expand macro="citations" />
89
90 </tool> 80 </tool>