Mercurial > repos > iuc > cnvkit_export_cdt

comparison cdt.xml @ 1:01066db437bf 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 11:51:21 +0000
parents 8834638e3248
children
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0:8834638e3248 1:01066db437bf
11 cnvkit.py export cdt 11 cnvkit.py export cdt
12 ./sample.cnr 12 ./sample.cnr
13 --output sample.cnv.cdt 13 --output sample.cnv.cdt
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="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" /> 19 <data name="CNVs_cdt" format="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" />
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_cdt" file="sample.cnv.cdt" /> 24 <output name="CNVs_cdt" file="sample.cnv.cdt" />
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 CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering. 28 This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering.
29 The conversion enables efficient exploration and interpretation of genomic copy number variations. 29 The conversion enables efficient exploration and interpretation of genomic copy number variations.
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>