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comparison read_distribution.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 5968573462fa
children
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62:473382134e56 63:27e16a30667a
2 <description>calculates how mapped reads were distributed over genome feature</description> 2 <description>calculates how mapped reads were distributed over genome feature</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_distribution.py --version]]></version_command> 9 <version_command><![CDATA[read_distribution.py --version]]></version_command>
13
14 <command><![CDATA[ 10 <command><![CDATA[
15 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
16 read_distribution.py -i 'input.${extension}' -r '${refgene}' > '${output}' 12 read_distribution.py -i 'input.${extension}' -r '${refgene}' > '${output}'
17 ]]> 13 ]]>
18 </command> 14 </command>
19
20 <inputs> 15 <inputs>
21 <expand macro="bam_sam_param" /> 16 <expand macro="bam_sam_param"/>
22 <expand macro="refgene_param" /> 17 <expand macro="refgene_param"/>
23 </inputs> 18 </inputs>
24
25 <outputs> 19 <outputs>
26 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/> 20 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/>
27 </outputs> 21 </outputs>
28
29 <tests> 22 <tests>
30 <test> 23 <test expect_num_outputs="1">
31 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 24 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
32 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 25 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
33 <output name="output" file="output.read_distribution.txt"/> 26 <output name="output" file="output.read_distribution.txt"/>
34 </test> 27 </test>
35 </tests> 28 </tests>
36
37 <help><![CDATA[ 29 <help><![CDATA[
38 read_distribution.py 30 read_distribution.py
39 ++++++++++++++++++++ 31 ++++++++++++++++++++
40 32
41 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped 33 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped
89 81
90 @ABOUT@ 82 @ABOUT@
91 83
92 ]]> 84 ]]>
93 </help> 85 </help>
94 86 <expand macro="citations"/>
95 <expand macro="citations" />
96
97 </tool> 87 </tool>