Mercurial > repos > iuc > cnvkit_scatter

comparison scatter.xml @ 5:64960243c9e1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 12:04:46 +0000
parents 02446206f574
children
comparison
equal deleted inserted replaced
4:f96c79d645b6 5:64960243c9e1
70 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq) 70 #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
71 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq 71 --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
72 #end if 72 #end if
73 ]]></command> 73 ]]></command>
74 <inputs> 74 <inputs>
75 <param name="input_cnr_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="" /> 75 <param name="input_cnr_file" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
76 <section name="advanced_settings" title="Advanced settings" expanded="false"> 76 <section name="advanced_settings" title="Advanced settings" expanded="false">
77 <expand macro="scatter_optional" /> 77 <expand macro="scatter_optional" />
78 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false"> 78 <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
79 <expand macro="scatter_plot" /> 79 <expand macro="scatter_plot" />
80 </section> 80 </section>
86 <outputs> 86 <outputs>
87 <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" /> 87 <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" />
88 </outputs> 88 </outputs>
89 <tests> 89 <tests>
90 <test expect_num_outputs="1"> 90 <test expect_num_outputs="1">
91 <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" /> 91 <param name="input_cnr_file" ftype="cnr" value="tumor.cnr" />
92 <section name="advanced_settings"> 92 <section name="advanced_settings">
93 <section name="additional_SNP_allelic_process"> 93 <section name="additional_SNP_allelic_process">
94 <param name="zygosity_freq" value="0.25" /> 94 <param name="zygosity_freq" value="0.25" />
95 </section> 95 </section>
96 <section name="plot_aesthetics"> 96 <section name="plot_aesthetics">
103 </test> 103 </test>
104 </tests> 104 </tests>
105 <help><![CDATA[ 105 <help><![CDATA[
106 Plot bin-level log2 coverages and segmentation calls together. Without any further arguments, 106 Plot bin-level log2 coverages and segmentation calls together. Without any further arguments,
107 this plots the genome-wide copy number in a form familiar to those who have used array CGH. 107 this plots the genome-wide copy number in a form familiar to those who have used array CGH.
108
109 -----
110
111 **Bin-level log2 ratios (.cnr)**
112
113 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.
114
115 .. csv-table::
116 :header-rows: 0
117
118 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
119 "start","Start position of the bin."
120 "end","End position of the bin."
121 "gene","Gene name(s) overlapping the bin (if applicable)."
122 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
123 "depth","Average read depth in the bin."
124 "weight","Reliability weight of the bin (higher = more reliable)."
125
126 -----
127
128 **Segmented log2 ratios (.cns)**
129
130 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
131
132 .. csv-table::
133 :header-rows: 0
134
135 "chromosome","start, end: Genomic coordinates of the segment"
136 "gene","Gene(s) overlapping the segment."
137 "log2","Mean log2 ratio of the segment."
138 "probes","Mean log2 ratio of the segment."
139 "depth","Average read depth."
140 "weight","Reliability weight."
141 "p_value","Statistical confidence (lower = more significant)."
142
108 ]]></help> 143 ]]></help>
109 <expand macro="citations" /> 144 <expand macro="citations" />
110 </tool> 145 </tool>