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comparison bam_stat.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
3 reads mapping statistics for a provided BAM or SAM file. 3 reads mapping statistics for a provided 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[bam_stat.py --version]]></version_command> 11 <version_command><![CDATA[bam_stat.py --version]]></version_command>
16
17 <command><![CDATA[ 12 <command><![CDATA[
18 @BAM_SAM_INPUTS@ 13 @BAM_SAM_INPUTS@
19 bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}' 14 bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}'
20 ]]> 15 ]]>
21 </command> 16 </command>
22
23 <inputs> 17 <inputs>
24 <expand macro="bam_sam_param" /> 18 <expand macro="bam_sam_param"/>
25 <expand macro="mapq_param" /> 19 <expand macro="mapq_param"/>
26 </inputs> 20 </inputs>
27
28 <outputs> 21 <outputs>
29 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/> 22 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/>
30 </outputs> 23 </outputs>
31
32 <tests> 24 <tests>
33 <test> 25 <test>
34 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 26 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
35 <output name="output" file="output.bamstats.txt" /> 27 <output name="output" file="output.bamstats.txt"/>
36 </test> 28 </test>
37 </tests> 29 </tests>
38
39 <help><![CDATA[ 30 <help><![CDATA[
40 bam_stat.py 31 bam_stat.py
41 +++++++++++ 32 +++++++++++
42 33
43 This program is used to calculate reads mapping statistics from provided BAM 34 This program is used to calculate reads mapping statistics from provided BAM
66 57
67 @ABOUT@ 58 @ABOUT@
68 59
69 ]]> 60 ]]>
70 </help> 61 </help>
71 62 <expand macro="citations"/>
72 <expand macro="citations" />
73 </tool> 63 </tool>