Mercurial > repos > iuc > cnvkit_breaks

comparison breaks.xml @ 3:9ff8e2b2cca1 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 11:48:14 +0000
parents 382f61e50156
children
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2:88b9d9aaa04f 3:9ff8e2b2cca1
16 #if $min_probes 16 #if $min_probes
17 --min-probes $min_probes 17 --min-probes $min_probes
18 #end if 18 #end if
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <inputs>
21 <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" /> 21 <param name="input_filename_file" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" />
22 <param name="input_segment_file" type="data" format="tabular" label="CN segmentation calls cnn file" help="The output of the CNVkit segment" /> 22 <param name="input_segment_file" type="data" format="cns" label="CN segmentation calls cns file" help="The output of the CNVkit segment" />
23 <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" /> 23 <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" />
24 </inputs> 24 </inputs>
25 <outputs> 25 <outputs>
26 <data name="gene_breaks" format="txt" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" /> 26 <data name="gene_breaks" format="txt" label="${tool.name} on ${on_string}:genes with copy number breakpoints" from_work_dir="gene-breaks.txt" />
27 </outputs> 27 </outputs>
28 <tests> 28 <tests>
29 <test expect_num_outputs="1"> 29 <test expect_num_outputs="1">
30 <param name="input_filename_file" ftype="tabular" value="sample.cnr" /> 30 <param name="input_filename_file" ftype="cnr" value="sample.cnr" />
31 <param name="input_segment_file" ftype="tabular" value="sample.cns" /> 31 <param name="input_segment_file" ftype="cns" value="sample.cns" />
32 <param name="min_probes" value="1" /> 32 <param name="min_probes" value="1" />
33 <output name="gene_breaks"> 33 <output name="gene_breaks">
34 <assert_contents><has_text text="chromosome"/></assert_contents> 34 <assert_contents><has_text text="chromosome"/></assert_contents>
35 </output> 35 </output>
36 </test> 36 </test>
41 (I) an unbalanced fusion or other structural rearrangement breakpoint occured 41 (I) an unbalanced fusion or other structural rearrangement breakpoint occured
42 (II) CNV calling is simply difficult due to an inconsistent copy number signal 42 (II) CNV calling is simply difficult due to an inconsistent copy number signal
43 43
44 The breaks output is a text table of tab-separated values, which is amenable to further processing by 44 The breaks output is a text table of tab-separated values, which is amenable to further processing by
45 scripts and standard Unix tools such as grep, sort, cut and awk. 45 scripts and standard Unix tools such as grep, sort, cut and awk.
46
47 -----
48
49 **Bin-level log2 ratios (.cnr)**
50
51 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.
52
53 .. csv-table::
54 :header-rows: 0
55
56 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
57 "start","Start position of the bin."
58 "end","End position of the bin."
59 "gene","Gene name(s) overlapping the bin (if applicable)."
60 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
61 "depth","Average read depth in the bin."
62 "weight","Reliability weight of the bin (higher = more reliable)."
63
64 -----
65
66 **Segmented log2 ratios (.cns)**
67
68 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
69
70 .. csv-table::
71 :header-rows: 0
72
73 "chromosome","start, end: Genomic coordinates of the segment"
74 "gene","Gene(s) overlapping the segment."
75 "log2","Mean log2 ratio of the segment."
76 "probes","Mean log2 ratio of the segment."
77 "depth","Average read depth."
78 "weight","Reliability weight."
79 "p_value","Statistical confidence (lower = more significant)."
80
46 ]]></help> 81 ]]></help>
47 <expand macro="citations" /> 82 <expand macro="citations" />
48 </tool> 83 </tool>
49 84
50 85