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comparison infer_experiment.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
1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>speculates how RNA-seq were configured</description> 2 <description>speculates how RNA-seq were configured</description>
3 <macros> 3 <macros>
4 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
5 </macros> 5 </macros>
6
7 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
8 7 <expand macro="requirements"/>
9 <expand macro="requirements" /> 8 <expand macro="stdio"/>
10
11 <expand macro="stdio" />
12
13 <version_command><![CDATA[infer_experiment.py --version]]></version_command> 9 <version_command><![CDATA[infer_experiment.py --version]]></version_command>
14
15 <command><![CDATA[ 10 <command><![CDATA[
16 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
17 infer_experiment.py -i 'input.${extension}' -r '${refgene}' 12 infer_experiment.py -i 'input.${extension}' -r '${refgene}'
18 --sample-size ${sample_size} 13 --sample-size ${sample_size}
19 --mapq ${mapq} 14 --mapq ${mapq}
20 > '${output}' 15 > '${output}'
21 ]]> 16 ]]>
22 </command> 17 </command>
23
24 <inputs> 18 <inputs>
25 <expand macro="bam_param" /> 19 <expand macro="bam_param"/>
26 <expand macro="refgene_param" /> 20 <expand macro="refgene_param"/>
27 <expand macro="sample_size_param" /> 21 <expand macro="sample_size_param"/>
28 <expand macro="mapq_param" /> 22 <expand macro="mapq_param"/>
29 </inputs> 23 </inputs>
30
31 <outputs> 24 <outputs>
32 <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" /> 25 <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration"/>
33 </outputs> 26 </outputs>
34
35 <tests> 27 <tests>
36 <test> 28 <test expect_num_outputs="1">
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 29 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
38 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 30 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
39 <output name="output" file="output.infer_experiment.txt"/> 31 <output name="output" file="output.infer_experiment.txt"/>
40 </test> 32 </test>
41 </tests> 33 </tests>
42
43 <help><![CDATA[ 34 <help><![CDATA[
44 infer_experiment.py 35 infer_experiment.py
45 +++++++++++++++++++ 36 +++++++++++++++++++
46 37
47 This program is used to speculate how RNA-seq sequencing were configured, especially how 38 This program is used to speculate how RNA-seq sequencing were configured, especially how
135 126
136 @ABOUT@ 127 @ABOUT@
137 128
138 ]]> 129 ]]>
139 </help> 130 </help>
140 131 <expand macro="citations"/>
141 <expand macro="citations" />
142
143 </tool> 132 </tool>