Mercurial > repos > iuc > cnvkit_segment

comparison segment.xml @ 4:5051e0f61b47 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 11:56:31 +0000
parents d5b444c208dd
children
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3:4318a3068879 4:5051e0f61b47
48 #if str($additional_SNP_allelic_process.zygosity_freq) 48 #if str($additional_SNP_allelic_process.zygosity_freq)
49 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq 49 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
50 #end if 50 #end if
51 ]]></command> 51 ]]></command>
52 <inputs> 52 <inputs>
53 <param name="filename" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" /> 53 <param name="filename" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
54 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false"> 54 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
55 <expand macro="additionally_SNP_process" /> 55 <expand macro="additionally_SNP_process" />
56 </section> 56 </section>
57 <section name="advanced_settings" title="Advanced settings" expanded="false"> 57 <section name="advanced_settings" title="Advanced settings" expanded="false">
58 <expand macro="segment_optional" /> 58 <expand macro="segment_optional" />
59 </section> 59 </section>
60 </inputs> 60 </inputs>
61 <outputs> 61 <outputs>
62 <data name="out_sample_segment" format="tabular" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" /> 62 <data name="out_sample_segment" format="cns" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
63 </outputs> 63 </outputs>
64 <tests> 64 <tests>
65 <test expect_num_outputs="1"> 65 <test expect_num_outputs="1">
66 <param name="filename" ftype="tabular" value="tumor.cnr" /> 66 <param name="filename" ftype="cnr" value="tumor.cnr" />
67 <section name="advanced_settings"> 67 <section name="advanced_settings">
68 <param name="method" value="hmm" /> 68 <param name="method" value="hmm" />
69 <param name="threshold" value="2" /> 69 <param name="threshold" value="2" />
70 <param name="drop_outliers" value="2" /> 70 <param name="drop_outliers" value="2" />
71 <param name="drop_low_coverage" value="1" /> 71 <param name="drop_low_coverage" value="1" />
79 Infer copy number segments from the given coverage table. Segmentation runs independently on 79 Infer copy number segments from the given coverage table. Segmentation runs independently on
80 each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch 80 each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
81 81
82 Segmented log2 ratios (.cns) output file contains those columns 82 Segmented log2 ratios (.cns) output file contains those columns
83 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes) 83 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
84
85 -----
86
87 **Bin-level log2 ratios (.cnr)**
88
89 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.
90
91 .. csv-table::
92 :header-rows: 0
93
94 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
95 "start","Start position of the bin."
96 "end","End position of the bin."
97 "gene","Gene name(s) overlapping the bin (if applicable)."
98 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
99 "depth","Average read depth in the bin."
100 "weight","Reliability weight of the bin (higher = more reliable)."
101
102 -----
103
104 **Segmented log2 ratios (.cns)**
105
106 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
107
108 .. csv-table::
109 :header-rows: 0
110
111 "chromosome","start, end: Genomic coordinates of the segment"
112 "gene","Gene(s) overlapping the segment."
113 "log2","Mean log2 ratio of the segment."
114 "probes","Mean log2 ratio of the segment."
115 "depth","Average read depth."
116 "weight","Reliability weight."
117 "p_value","Statistical confidence (lower = more significant)."
118
84 ]]></help> 119 ]]></help>
85 <expand macro="citations" /> 120 <expand macro="citations" />
86 </tool> 121 </tool>