Mercurial > repos > iuc > cnvkit_call

comparison call.xml @ 5:e570209e97bf 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 11:53:55 +0000
parents b7b790a1cae0
children
comparison
equal deleted inserted replaced
4:8ac43ea6e763 5:e570209e97bf
70 #if str($additional_SNP_allelic_process.zygosity_freq) 70 #if str($additional_SNP_allelic_process.zygosity_freq)
71 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq 71 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
72 #end if 72 #end if
73 ]]></command> 73 ]]></command>
74 <inputs> 74 <inputs>
75 <param name="input_sample_file" type="data" format="tabular" label="CN segmentation calls cns file" help="" /> 75 <param name="input_sample_file" type="data" format="cns" label="CN segmentation calls cns file" help="" />
76 <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false"> 76 <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false">
77 <expand macro="additionally_SNP_process" /> 77 <expand macro="additionally_SNP_process" />
78 </section> 78 </section>
79 <section name="advanced_settings" title="Advanced settings" expanded="false"> 79 <section name="advanced_settings" title="Advanced settings" expanded="false">
80 <expand macro="call_optional" /> 80 <expand macro="call_optional" />
91 </when> 91 </when>
92 </conditional> 92 </conditional>
93 </section> 93 </section>
94 </inputs> 94 </inputs>
95 <outputs> 95 <outputs>
96 <data name="out_sample_Bintest" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" /> 96 <data name="out_sample_Bintest" format="cns" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
97 </outputs> 97 </outputs>
98 <tests> 98 <tests>
99 <test expect_num_outputs="1"> 99 <test expect_num_outputs="1">
100 <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> 100 <param name="input_sample_file" ftype="cns" value="tumor.cns" />
101 <section name="additional_SNP_allelic_process"> 101 <section name="additional_SNP_allelic_process">
102 <param name="zygosity_freq" value="0.25" /> 102 <param name="zygosity_freq" value="0.25" />
103 <param name="min_variant_depth" value="40" /> 103 <param name="min_variant_depth" value="40" />
104 </section> 104 </section>
105 <section name="advanced_settings"> 105 <section name="advanced_settings">
114 <conditional name="Sample_sex"> 114 <conditional name="Sample_sex">
115 <param name="sex" value="yes" /> 115 <param name="sex" value="yes" />
116 </conditional> 116 </conditional>
117 <param name="purity" value="1" /> 117 <param name="purity" value="1" />
118 </section> 118 </section>
119 <param name="input_sample_file" ftype="tabular" value="tumor.cns" /> 119 <param name="input_sample_file" ftype="cns" value="tumor.cns" />
120 <section name="additional_SNP_allelic_process"> 120 <section name="additional_SNP_allelic_process">
121 <param name="min_variant_depth" value="40" /> 121 <param name="min_variant_depth" value="40" />
122 </section> 122 </section>
123 <output name="out_sample_Bintest"> 123 <output name="out_sample_Bintest">
124 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 124 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
130 A list of threshold log2 values for each copy number state (-m threshold), or rescaling - for a given known 130 A list of threshold log2 values for each copy number state (-m threshold), or rescaling - for a given known
131 tumor cell fraction and normal ploidy, then simple rounding to the nearest integer copy number (-m clonal). 131 tumor cell fraction and normal ploidy, then simple rounding to the nearest integer copy number (-m clonal).
132 132
133 The output is Segmented log2 ratios (.cns) file with those columns 133 The output is Segmented log2 ratios (.cns) file with those columns
134 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes) 134 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
135
136 -----
137
138 **Segmented log2 ratios (.cns)**
139
140 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
141
142 .. csv-table::
143 :header-rows: 0
144
145 "chromosome","start, end: Genomic coordinates of the segment"
146 "gene","Gene(s) overlapping the segment."
147 "log2","Mean log2 ratio of the segment."
148 "probes","Mean log2 ratio of the segment."
149 "depth","Average read depth."
150 "weight","Reliability weight."
151 "p_value","Statistical confidence (lower = more significant)."
135 ]]></help> 152 ]]></help>
136 <expand macro="citations" /> 153 <expand macro="citations" />
137 </tool> 154 </tool>