Mercurial > repos > iuc > cnvkit_export_jtv

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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 11:50:29 +0000
parents 31a7f5d994f1
children
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0:31a7f5d994f1 1:fd81cbc8cd33
11 cnvkit.py export jtv 11 cnvkit.py export jtv
12 ./sample.cnr 12 ./sample.cnr
13 --output sample.cnv.jtv 13 --output sample.cnv.jtv
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" 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_cdt" format="jtv" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.jtv" /> 19 <data name="CNVs_cdt" format="jtv" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.jtv" />
20 </outputs> 20 </outputs>
21 <tests> 21 <tests>
25 </test> 25 </test>
26 </tests> 26 </tests>
27 <help><![CDATA[ 27 <help><![CDATA[
28 This tool converts CNVkit log2 copy ratio data to Java TreeView's native format (.jtv), 28 This tool converts CNVkit log2 copy ratio data to Java TreeView's native format (.jtv),
29 enabling easy visualisation and clustering analysis with preserved settings for seamless data exploration. 29 enabling easy visualisation and clustering analysis with preserved settings for seamless data exploration.
30
31 -----
32
33 **Bin-level log2 ratios (.cnr)**
34
35 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.
36
37 .. csv-table::
38 :header-rows: 0
39
40 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
41 "start","Start position of the bin."
42 "end","End position of the bin."
43 "gene","Gene name(s) overlapping the bin (if applicable)."
44 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
45 "depth","Average read depth in the bin."
46 "weight","Reliability weight of the bin (higher = more reliable)."
47
48
30 ]]></help> 49 ]]></help>
31 <expand macro="citations" /> 50 <expand macro="citations" />
32 </tool> 51 </tool>