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comparison facets_analysis.xml @ 3:d1914f4d9daf draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
author artbio
date Sun, 05 Oct 2025 00:55:34 +0000
parents 66a56502199d
children 3f62267c4be7
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2:66a56502199d 3:d1914f4d9daf
9 Rscript '${__tool_directory__}/facets_analysis.R' 9 Rscript '${__tool_directory__}/facets_analysis.R'
10 --pileup '$pileup' 10 --pileup '$pileup'
11 --sample_id '$pileup.name' 11 --sample_id '$pileup.name'
12 --output_seg '$output_seg' 12 --output_seg '$output_seg'
13 --output_summary '$output_summary' 13 --output_summary '$output_summary'
14 --output_spider '$output_spider'
14 --output_plots '$output_plots' 15 --output_plots '$output_plots'
15 --cval $cval 16 --cval $cval
16 --min_nhet $min_nhet 17 --min_nhet $min_nhet
17 --snp_nbhd $snp_nbhd 18 --snp_nbhd $snp_nbhd
18 --gbuild '$gbuild' 19 --gbuild '$gbuild'
34 <param name="snp_nbhd" type="integer" value="300" label="SNP neighborhood size (snp.nbhd)" help="Should match the --pseudo-snps distance used to generate the pileup file. Default is 300."/> 35 <param name="snp_nbhd" type="integer" value="300" label="SNP neighborhood size (snp.nbhd)" help="Should match the --pseudo-snps distance used to generate the pileup file. Default is 300."/>
35 </inputs> 36 </inputs>
36 <outputs> 37 <outputs>
37 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/> 38 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
38 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/> 39 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
39 <data name="output_plots" format="pdf" label="FACETS Plots on ${on_string}"/> 40 <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/>
41 <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/>
42
40 </outputs> 43 </outputs>
41 <tests> 44 <tests>
42 <test> 45 <test>
43 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/> 46 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
44 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/> 47 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
45 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/> 48 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
46 <output name="output_plots" file="test_sample_01.plots.pdf" ftype="pdf" compare="sim_size" delta="1000"/> 49 <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/>
50 <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/>
47 </test> 51 </test>
48 </tests> 52 </tests>
49 <help><![CDATA[ 53 <help><![CDATA[
50 **What it does** 54 **What it does**
51 55