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comparison junction_annotation.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
1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> 1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>compares detected splice junctions to reference gene model</description> 2 <description>compares detected splice junctions to reference gene model</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
9 <expand macro="requirements"> 7 <expand macro="requirements">
10 <!-- 8 <!--
11 Required due to conda solver bug: https://github.com/conda/conda/issues/6269 9 Required due to conda solver bug: https://github.com/conda/conda/issues/6269
12 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info 10 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
13 --> 11 -->
14 <requirement type="package" version="4.2.2">r-base</requirement> 12 <requirement type="package" version="4.2.2">r-base</requirement>
15 </expand> 13 </expand>
16 14 <expand macro="stdio"/>
17 <expand macro="stdio" />
18
19 <version_command><![CDATA[junction_annotation.py --version]]></version_command> 15 <version_command><![CDATA[junction_annotation.py --version]]></version_command>
20
21 <command><![CDATA[ 16 <command><![CDATA[
22 @BAM_SAM_INPUTS@ 17 @BAM_SAM_INPUTS@
23 junction_annotation.py 18 junction_annotation.py
24 --input-file 'input.${extension}' 19 --input-file 'input.${extension}'
25 --refgene '${refgene}' 20 --refgene '${refgene}'
27 --min-intron ${min_intron} 22 --min-intron ${min_intron}
28 --mapq ${mapq} 23 --mapq ${mapq}
29 2> >(tee -a stats.txt >&2) 24 2> >(tee -a stats.txt >&2)
30 ]]> 25 ]]>
31 </command> 26 </command>
32
33 <inputs> 27 <inputs>
34 <expand macro="bam_sam_param" /> 28 <expand macro="bam_sam_param"/>
35 <expand macro="refgene_param" /> 29 <expand macro="refgene_param"/>
36 <expand macro="min_intron_param" /> 30 <expand macro="min_intron_param"/>
37 <expand macro="mapq_param" /> 31 <expand macro="mapq_param"/>
38 <expand macro="rscript_output_param" /> 32 <expand macro="rscript_output_param"/>
39 </inputs> 33 </inputs>
40
41 <outputs> 34 <outputs>
42 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/> 35 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
43 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" /> 36 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)"/>
44 <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" /> 37 <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)"/>
45 <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/> 38 <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
46 <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" /> 39 <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats"/>
47 </outputs> 40 </outputs>
48
49 <tests> 41 <tests>
50 <test> 42 <test expect_num_outputs="5">
51 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 43 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
52 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> 44 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
53 <param name="rscript_output" value="true" /> 45 <param name="rscript_output" value="true"/>
54 <output name="outputxls" file="output.junction.xls" ftype="tabular"/> 46 <output name="outputxls" file="output.junction.xls" ftype="tabular"/>
55 <output name="outputr" file="output.junction_plot_r" /> 47 <output name="outputr" file="output.junction_plot_r"/>
56 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> 48 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size"/>
57 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" /> 49 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size"/>
58 <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" /> 50 <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2"/>
59 </test> 51 </test>
60 </tests> 52 </tests>
61
62 <help><![CDATA[ 53 <help><![CDATA[
63 junction_annotation.py 54 junction_annotation.py
64 ++++++++++++++++++++++ 55 ++++++++++++++++++++++
65 56
66 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED 57 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
110 101
111 @ABOUT@ 102 @ABOUT@
112 103
113 ]]> 104 ]]>
114 </help> 105 </help>
115 106 <expand macro="citations"/>
116 <expand macro="citations" />
117
118 </tool> 107 </tool>