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comparison reference.xml @ 5:096341b06bfe 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 11:52:50 +0000
parents b551442cf2a0
children
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4:d54e2e021402 5:096341b06bfe
79 <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false"> 79 <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
80 <expand macro="disable_specific_automatic_bias_corrections" /> 80 <expand macro="disable_specific_automatic_bias_corrections" />
81 </section> 81 </section>
82 </when> 82 </when>
83 <when value="yes"> 83 <when value="yes">
84 <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="Sample Target/antitarget Coverage cnn file" help="" /> 84 <param name="input_cnn_file" type="data" format="cnn" multiple="true" label="Sample Target/antitarget Coverage cnn file" help="" />
85 <section name="advanced_settings" title="Advanced settings" expanded="false"> 85 <section name="advanced_settings" title="Advanced settings" expanded="false">
86 <expand macro="reference_interface" /> 86 <expand macro="reference_interface" />
87 <expand macro="reference_optional" /> 87 <expand macro="reference_optional" />
88 <expand macro="sample_sex_condition" /> 88 <expand macro="sample_sex_condition" />
89 </section> 89 </section>
92 </section> 92 </section>
93 </when> 93 </when>
94 </conditional> 94 </conditional>
95 </inputs> 95 </inputs>
96 <outputs> 96 <outputs>
97 <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" /> 97 <data name="out_referene_tas" format="cnn" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
98 </outputs> 98 </outputs>
99 <tests> 99 <tests>
100 <test expect_num_outputs="1"> 100 <test expect_num_outputs="1">
101 <conditional name="CNV_reference"> 101 <conditional name="CNV_reference">
102 <param name="CNV_reference_availabel" value="yes" /> 102 <param name="CNV_reference_availabel" value="yes" />
104 <conditional name="reference_source"> 104 <conditional name="reference_source">
105 <param name="ref_selector" value="history"/> 105 <param name="ref_selector" value="history"/>
106 <param name="fasta" ftype="fasta" value="genome.fasta" /> 106 <param name="fasta" ftype="fasta" value="genome.fasta" />
107 </conditional> 107 </conditional>
108 </section> 108 </section>
109 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> 109 <param name="input_cnn_file" ftype="cnn" value="tumor.targetcoverage.cnn" />
110 <section name="disable_some_of_the_bias_corrections"> 110 <section name="disable_some_of_the_bias_corrections">
111 <param name="no_gc" value="1" /> 111 <param name="no_gc" value="1" />
112 </section> 112 </section>
113 </conditional> 113 </conditional>
114 <output name="out_referene_tas" file="ref-tas.cnn" /> 114 <output name="out_referene_tas" file="ref-tas.cnn" />
120 <conditional name="reference_source"> 120 <conditional name="reference_source">
121 <param name="ref_selector" value="cached"/> 121 <param name="ref_selector" value="cached"/>
122 <param name="fasta" value="test_buildid"/> 122 <param name="fasta" value="test_buildid"/>
123 </conditional> 123 </conditional>
124 </section> 124 </section>
125 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" /> 125 <param name="input_cnn_file" ftype="cnn" value="tumor.targetcoverage.cnn" />
126 <section name="disable_some_of_the_bias_corrections"> 126 <section name="disable_some_of_the_bias_corrections">
127 <param name="no_gc" value="1" /> 127 <param name="no_gc" value="1" />
128 </section> 128 </section>
129 </conditional> 129 </conditional>
130 <output name="out_referene_tas" file="ref-tas.cnn" /> 130 <output name="out_referene_tas" file="ref-tas.cnn" />
136 <conditional name="reference_source"> 136 <conditional name="reference_source">
137 <param name="ref_selector" value="cached"/> 137 <param name="ref_selector" value="cached"/>
138 <param name="fasta" value="test_buildid"/> 138 <param name="fasta" value="test_buildid"/>
139 </conditional> 139 </conditional>
140 </section> 140 </section>
141 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" /> 141 <param name="input_cnn_file" ftype="cnn" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
142 <section name="disable_some_of_the_bias_corrections"> 142 <section name="disable_some_of_the_bias_corrections">
143 <param name="no_gc" value="1" /> 143 <param name="no_gc" value="1" />
144 </section> 144 </section>
145 </conditional> 145 </conditional>
146 <output name="out_referene_tas"> 146 <output name="out_referene_tas">
194 194
195 The reference .cnn file output contains those columns 195 The reference .cnn file output contains those columns
196 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion 196 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
197 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage 197 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
198 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth) 198 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
199 199
200 -----
201
202 **Copy Number Reference Profile (.cnn)**
203
204 Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
205
206 .. csv-table::
207 :header-rows: 0
208
209 "chromosome","Genomic chromosome (e.g., chr1, chrX)."
210 "start","Start position of the bin."
211 "end","End position of the bin."
212 "gene","Gene name(s) (if applicable)."
213 "log2","Reference log2 ratio (typically 0 for diploid regions)."
214 "depth","Average read depth across control samples."
215 "spread","Variability (standard deviation) of coverage in controls."
216
217 -----
218
219 **Target Coverage File (e.g., sample.targetcoverage.cnn):**
220
221 - **Columns:** chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size).
222
223 - **Purpose:** Captures on-target sequencing depth.
224
200 ]]></help> 225 ]]></help>
201 <expand macro="citations" /> 226 <expand macro="citations" />
202 </tool> 227 </tool>