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comparison junction_annotation.xml @ 61:5968573462fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:23:05 +0000
parents 1421603cc95b
children 473382134e56
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60:1421603cc95b 61:5968573462fa
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 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
6 </macros> 5 </macros>
6
7 <expand macro="bio_tools"/>
7 8
8 <expand macro="requirements"> 9 <expand macro="requirements">
9 <!-- 10 <!--
10 Required due to conda solver bug: https://github.com/conda/conda/issues/6269 11 Required due to conda solver bug: https://github.com/conda/conda/issues/6269
11 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info 12 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
23 --input-file 'input.${extension}' 24 --input-file 'input.${extension}'
24 --refgene '${refgene}' 25 --refgene '${refgene}'
25 --out-prefix output 26 --out-prefix output
26 --min-intron ${min_intron} 27 --min-intron ${min_intron}
27 --mapq ${mapq} 28 --mapq ${mapq}
29 2> >(tee -a stats.txt >&2)
28 ]]> 30 ]]>
29 </command> 31 </command>
30 32
31 <inputs> 33 <inputs>
32 <expand macro="bam_sam_param" /> 34 <expand macro="bam_sam_param" />
35 <expand macro="mapq_param" /> 37 <expand macro="mapq_param" />
36 <expand macro="rscript_output_param" /> 38 <expand macro="rscript_output_param" />
37 </inputs> 39 </inputs>
38 40
39 <outputs> 41 <outputs>
40 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/> 42 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
41 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" /> 43 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" />
42 <expand macro="xls_output_data" filename="output.junction.xls" /> 44 <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" />
43 <expand macro="rscript_output_data" filename="output.junction_plot.r" /> 45 <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
46 <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" />
44 </outputs> 47 </outputs>
45 48
46 <tests> 49 <tests>
47 <test> 50 <test>
48 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 51 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
50 <param name="rscript_output" value="true" /> 53 <param name="rscript_output" value="true" />
51 <output name="outputxls" file="output.junction.xls" /> 54 <output name="outputxls" file="output.junction.xls" />
52 <output name="outputr" file="output.junction_plot_r" /> 55 <output name="outputr" file="output.junction_plot_r" />
53 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> 56 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
54 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" /> 57 <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" />
55 </test> 59 </test>
56 </tests> 60 </tests>
57 61
58 <help><![CDATA[ 62 <help><![CDATA[
59 junction_annotation.py 63 junction_annotation.py