Mercurial > repos > iuc > cnvkit_export_nexus_basic

comparison nexus_basic.xml @ 1:6dc05861aaea draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:52:29 +0000
parents eec611d7ef03
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0:eec611d7ef03 1:6dc05861aaea
11 cnvkit.py export nexus-basic 11 cnvkit.py export nexus-basic
12 ./sample.cnr 12 ./sample.cnr
13 --output sample.cnv.tsv 13 --output sample.cnv.tsv
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" /> 16 <param name="input_segmented_file" type="data" format="cnr,cns" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
17 </inputs> 17 </inputs>
18 <outputs> 18 <outputs>
19 <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" /> 19 <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" />
20 </outputs> 20 </outputs>
21 <tests> 21 <tests>
22 <test expect_num_outputs="1"> 22 <test expect_num_outputs="1">
23 <param name="input_segmented_file" ftype="tabular" value="sample.cnr" /> 23 <param name="input_segmented_file" ftype="cnr" value="sample.cnr" />
24 <output name="CNVs_NexusBasic" file="sample.cnv.tsv" /> 24 <output name="CNVs_NexusBasic" file="sample.cnv.tsv" />
25 </test> 25 </test>
26 </tests> 26 </tests>
27 <help><![CDATA[ 27 <help><![CDATA[
28 This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format, 28
29 enabling efficient visualisation and analysis of genomic alterations in Nexus software. 29 This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format,
30 This conversion facilitates downstream interpretation and integration with other genomic data. 30 enabling efficient visualisation and analysis of genomic alterations in Nexus software.
31 This conversion facilitates downstream interpretation and integration with other genomic data.
32
33 -----
34
35 **Bin-level log2 ratios (.cnr)**
36
37 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
38
39 .. csv-table::
40 :header-rows: 0
41
42 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
43 "start","Start position of the bin."
44 "end","End position of the bin."
45 "gene","Gene name(s) overlapping the bin (if applicable)."
46 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
47 "depth","Average read depth in the bin."
48 "weight","Reliability weight of the bin (higher = more reliable)."
49
31 ]]></help> 50 ]]></help>
32 <expand macro="citations" /> 51 <expand macro="citations" />
33 </tool> 52 </tool>