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comparison RNA_fragment_size.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
comparison
equal deleted inserted replaced
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[RNA_fragment_size.py --version]]></version_command> 11 <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command>
15
16 <command><![CDATA[ 12 <command><![CDATA[
17 @BAM_SAM_INPUTS@ 13 @BAM_SAM_INPUTS@
18 RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}' 14 RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
19 ]]> 15 ]]>
20 </command> 16 </command>
21
22 <inputs> 17 <inputs>
23 <expand macro="bam_param" /> 18 <expand macro="bam_param"/>
24 <expand macro="refgene_param" /> 19 <expand macro="refgene_param"/>
25 <expand macro="mapq_param" /> 20 <expand macro="mapq_param"/>
26 <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)" /> 21 <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)"/>
27 </inputs> 22 </inputs>
28
29 <outputs> 23 <outputs>
30 <data format="tabular" name="output" /> 24 <data format="tabular" name="output"/>
31 </outputs> 25 </outputs>
32
33 <tests> 26 <tests>
34 <test> 27 <test expect_num_outputs="1">
35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 28 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
36 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 29 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
37 <output name="output"> 30 <output name="output">
38 <assert_contents> 31 <assert_contents>
39 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" /> 32 <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$"/>
40 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" /> 33 <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$"/>
41 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" /> 34 <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$"/>
42 <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" /> 35 <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$"/>
43 <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" /> 36 <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$"/>
44 <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" /> 37 <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$"/>
45 <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" /> 38 <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$"/>
46 <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" /> 39 <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$"/>
47 </assert_contents> 40 </assert_contents>
48 </output> 41 </output>
49 </test> 42 </test>
50 </tests> 43 </tests>
51
52 <help><![CDATA[ 44 <help><![CDATA[
53 RNA_fragment_size.py 45 RNA_fragment_size.py
54 ++++++++++++++++++++ 46 ++++++++++++++++++++
55 47
56 Calculate fragment size for each gene/transcript. For each transcript, it will 48 Calculate fragment size for each gene/transcript. For each transcript, it will
78 @ABOUT@ 70 @ABOUT@
79 71
80 ]]> 72 ]]>
81 73
82 </help> 74 </help>
83 75 <expand macro="citations"/>
84 <expand macro="citations" />
85
86 </tool> 76 </tool>