Mercurial > repos > iuc > cnvkit_scatter

comparison macros.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
1 <macros> 1 <macros>
2 <token name="@VERSION_SUFFIX@">1</token> 2 <token name="@VERSION_SUFFIX@">0</token>
3 <token name="@TOOL_VERSION@">0.9.11</token> 3 <token name="@TOOL_VERSION@">0.9.12</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">cnvkit</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">cnvkit</requirement>
7 <requirement type="package" version="1.4.2">scikit-learn</requirement> 7 <requirement type="package" version="1.21">samtools</requirement>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
10 <xml name="reference_interface"> 10 <xml name="reference_interface">
11 <conditional name="reference_source"> 11 <conditional name="reference_source">
12 <param name="ref_selector" type="select" label="Choose the source for the reference genome"> 12 <param name="ref_selector" type="select" label="Choose the source for the reference genome">
54 <option value="hybrid" selected="True">hybridization capture </option> 54 <option value="hybrid" selected="True">hybridization capture </option>
55 <option value="amplicon">targeted amplicon sequencing </option> 55 <option value="amplicon">targeted amplicon sequencing </option>
56 <option value="wgs">whole genome sequencing </option> 56 <option value="wgs">whole genome sequencing </option>
57 </param> 57 </param>
58 <param argument="--segment-method" type="select" label="Method used in the 'segment' step" help=""> 58 <param argument="--segment-method" type="select" label="Method used in the 'segment' step" help="">
59 <option value="cbs" selected="True">Circular Binary Segmentation CBS</option> 59 <option value="cbs" selected="True">CBS: Circular Binary Segmentation (default, precise)</option>
60 <option value="flasso">Fused lasso, hybrid flasso</option> 60 <option value="flasso">Flasso: Fused Lasso; smoother segments, fewer breakpoints</option>
61 <option value="haar">a pure-Python implementation of HaarSeg, a wavelet-based method. Very fast and performs reasonably well on small panels, but tends to over-segment large datasets., hybrid haar</option> 61 <option value="haar">Haar: Haar wavelet transform; detects abrupt changes</option>
62 <option value="none">simply calculate the weighted mean log2 value of each chromosome arm. Useful for testing or debugging, or as a baseline for benchmarking other methods., hybrid none</option> 62 <option value="none">None: No segmentation; outputs bin-level data as segments</option>
63 <option value="hmm">experimental – a 3-state Hidden Markov Model suitable for most samples. Faster than CBS, and slower but more accurate than Haar. Requires the Python package pomegranate, as do the next two thods., hybrid hmm</option> 63 <option value="hmm">Hmm: Basic Hidden Markov Model (generic use)</option>
64 <option value="hmm-tumor">experimental – a 5-state HMM suitable for finer-grained segmentation of good-quality tumor samples. In particular, this method can detect focal amplifications within a larger-scale, smaller-amplitude copy number gain, or focal deep deletions within a larger-scale hemizygous loss. Training this model takes a bit more CPU time than the simpler hmm method., hybrid hmm-tumor</option> 64 <option value="hmm-tumor">Hmm-tumor: HMM tailored for tumor samples (somatic CNVs)</option>
65 <option value="hmm-germline">experimental – a 3-state HMM with fixed amplitude for the loss, neutral, and gain states corresponding to absolute copy numbers of 1, 2, and 3. Suitable for germline samples and single-cell sequencing of samples with mostly-diploid genomes that are not overly aneuploid., hybrid hmm-germline</option> 65 <option value="hmm-germline">Hmm-germline: HMM for germline (inherited) variants (diploid assumption)</option>
66 </param> 66 </param>
67 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Use or assume a male reference" help="female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX" /> 67 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Use or assume a male reference" help="female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX" />
68 <param argument="--countreads" type="boolean" checked="false" truevalue="--countreads" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" /> 68 <param argument="--countreads" type="boolean" checked="false" truevalue="--countreads" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
69 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" /> 69 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
70 </xml> 70 </xml>
71 <xml name="create_CNV_reference_file"> 71 <xml name="create_CNV_reference_file">
72 <param name="input_sample_file" type="data" format="bam" label="Sample BAM file" help="" /> 72 <param name="input_sample_file" type="data" format="bam" label="Sample BAM file" help="" />
73 <param argument="--normal" type="data" format="bam" label="Control BAM file" help="" /> 73 <param argument="--normal" optional="true" type="data" format="bam" label="Control BAM file" help="It is optional only if You have a single sample or are working with WGS data with no normal samples" />
74 <param argument="--targets" type="data" format="bed" label="Capture BED regions" help="" /> 74 <param argument="--targets" type="data" format="bed" label="Capture BED regions" help="" />
75 </xml> 75 </xml>
76 <xml name="advanced_no_reference"> 76 <xml name="advanced_no_reference">
77 <param argument="--antitargets" optional="true" type="data" format="bed,tabular" label="Antitarget intervals" help="BED or list" /> 77 <param argument="--antitargets" optional="true" type="data" format="bed,tabular" label="Antitarget intervals" help="BED or list" />
78 <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file preferred, or BED, interval list, GFF, or similar" /> 78 <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file preferred, or BED, interval list, GFF, or similar" />
83 <param argument="--antitarget-min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="" help="" /> 83 <param argument="--antitarget-min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="" help="" />
84 <param argument="--cluster" optional="true" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Calculate and use cluster-specific summary stats in the reference pool" help="" /> 84 <param argument="--cluster" optional="true" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Calculate and use cluster-specific summary stats in the reference pool" help="" />
85 </xml> 85 </xml>
86 <xml name="reuse_an_existing_cnv_reference_file"> 86 <xml name="reuse_an_existing_cnv_reference_file">
87 <param name="input_sample_file" type="data" format="bam" label="Sample file" help="" /> 87 <param name="input_sample_file" type="data" format="bam" label="Sample file" help="" />
88 <param argument="--reference" type="data" format="tabular" label="CNV reference CNN File" help="" /> 88 <param argument="--reference" type="data" format="cnn" label="CNV reference CNN File" help="" />
89 </xml> 89 </xml>
90 <xml name="output_section"> 90 <xml name="output_section">
91 <section name="output_section" title="Outputs" expanded="false"> 91 <section name="output_section" title="Outputs" expanded="false">
92 <param argument="--scatter" type="boolean" checked="false" truevalue="--scatter" falsevalue="" label="Create a whole-genome copy ratio profile as a PNG scatter plot" help="" /> 92 <param argument="--scatter" type="boolean" checked="false" truevalue="--scatter" falsevalue="" label="Create a whole-genome copy ratio profile as a PNG scatter plot" help="" />
93 <param argument="--diagram" type="boolean" checked="false" truevalue="--diagram" falsevalue="" label="Create an ideogram of copy ratios on chromosomes as a PDF" help="" /> 93 <param argument="--diagram" type="boolean" checked="false" truevalue="--diagram" falsevalue="" label="Create an ideogram of copy ratios on chromosomes as a PDF" help="" />
135 <option value="median" selected="True">median</option> 135 <option value="median" selected="True">median</option>
136 <option value="mode">mode</option> 136 <option value="mode">mode</option>
137 <option value="biweight">biweight</option> 137 <option value="biweight">biweight</option>
138 </param> 138 </param>
139 <param argument="--center-at" optional="true" type="float" label="Subtract a constant number from all log2 ratios" value="" help="For manual re-centering, in case the --center option gives unsatisfactory results" /> 139 <param argument="--center-at" optional="true" type="float" label="Subtract a constant number from all log2 ratios" value="" help="For manual re-centering, in case the --center option gives unsatisfactory results" />
140 <param argument="--thresholds" optional="true" type="text" label="Hard thresholds for calling each integer copy number, separated by commas" value="=-1.1,-0.25,0.2,0.7" help="Apply cutoffs to either original or rescaled log2 values" /> 140 <param argument="--thresholds" type="text" label="Hard thresholds for calling each integer copy number, separated by commas" value="=-1.1,-0.25,0.2,0.7" help="Apply cutoffs to either original or rescaled log2 values" />
141 <param argument="--ploidy" optional="true" type="integer" label="Ploidy of the sample cells" min="1" max="2" value="2" help="" /> 141 <param argument="--ploidy" optional="true" type="integer" label="Ploidy of the sample cells" min="1" max="2" value="2" help="" />
142 <param argument="--purity" optional="true" type="float" label="Estimated tumor cell fraction, a.k.a. purity or cellularity" min="0" max="1" value="" help="" /> 142 <param argument="--purity" optional="true" type="float" label="Estimated tumor cell fraction, a.k.a. purity or cellularity" min="0" max="1" value="" help="" />
143 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" /> 143 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
144 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Use or assume a male reference" help="Was a male reference used? If so, expect half ploidy on chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit, if a male reference was used, the neutral copy number ploidy of chrX is 1; chrY is haploid for either reference sex" /> 144 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Use or assume a male reference" help="Was a male reference used? If so, expect half ploidy on chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit, if a male reference was used, the neutral copy number ploidy of chrX is 1; chrY is haploid for either reference sex" />
145 </xml> 145 </xml>
146 <xml name="additionally_SNP_process"> 146 <xml name="additionally_SNP_process">
147 <param argument="--vcf" optional="true" type="data" format="vcf" label="VCF file" help="VCF file name containing variants for calculation of b-allele frequencies" /> 147 <param argument="--vcf" optional="true" type="data" format="vcf" label="VCF file" help="VCF file name containing variants for calculation of b-allele frequencies" />
148 <param argument="--sample-id" optional="true" type="text" label="Name of the sample in the VCF to use for b-allele frequency extraction" value="" help="" /> 148 <param argument="--sample-id" type="text" label="Name of the sample in the VCF to use for b-allele frequency extraction" help="" />
149 <param argument="--normal-id" optional="true" type="text" label="Corresponding normal sample ID in the input VCF" value="" help="This sample is used to select only germline SNVs to calculate b-allele frequencies" /> 149 <param argument="--normal-id" type="text" label="Corresponding normal sample ID in the input VCF" help="This sample is used to select only germline SNVs to calculate b-allele frequencies" />
150 <param argument="--min-variant-depth" type="integer" min="1" value="20" optional="true" label="Minimum read depth for a SNV to be used in the b-allele frequency calculation" help="" /> 150 <param argument="--min-variant-depth" type="integer" min="1" value="20" optional="true" label="Minimum read depth for a SNV to be used in the b-allele frequency calculation" help="" />
151 <param argument="--zygosity-freq" type="float" min="0" value="0.25" optional="true" label="Ignore VCF's genotypes and instead infer zygosity from allele frequencies" help="" /> 151 <param argument="--zygosity-freq" type="float" min="0" value="0.25" optional="true" label="Ignore VCF's genotypes and instead infer zygosity from allele frequencies" help="" />
152 </xml> 152 </xml>
153 <xml name="diagram_optional"> 153 <xml name="diagram_optional">
154 <param argument="--segment" optional="true" type="data" format="tabular" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" /> 154 <param argument="--segment" optional="true" type="data" format="cns,cnr" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" />
155 <param argument="--threshold" optional="true" type="float" label="Threshold" min="0" value="0.5" help="Copy number change threshold to label genes" /> 155 <param argument="--threshold" optional="true" type="float" label="Threshold" min="0" value="0.5" help="Copy number change threshold to label genes" />
156 <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" min="1" value="3" help="Minimum number of covered probes to label a gene" /> 156 <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" min="1" value="3" help="Minimum number of covered probes to label a gene" />
157 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" /> 157 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
158 <param argument="--no-shift-xy" type="boolean" checked="false" truevalue="--no-shift-xy" falsevalue="" label="Don't adjust the X and Y chromosomes according to sample sex" help="" /> 158 <param argument="--no-shift-xy" type="boolean" checked="false" truevalue="--no-shift-xy" falsevalue="" label="Don't adjust the X and Y chromosomes according to sample sex" help="" />
159 <param argument="--chromosome" optional="true" type="text" label="Chromosome to display" value="" help="e.g. 'chr1' no chromosomal range allowed" /> 159 <param argument="--chromosome" type="text" label="Chromosome to display" help="e.g. 'chr1' no chromosomal range allowed" />
160 </xml> 160 </xml>
161 <xml name="diagram_plot"> 161 <xml name="diagram_plot">
162 <param argument="--title" optional="true" type="text" label="Plot title" value="" help="" /> 162 <param argument="--title" type="text" label="Plot title" help="" />
163 <param argument="--no-gene-labels" type="boolean" checked="false" truevalue="--no-gene-labels" falsevalue="" label="Disable gene_name labels on plot useful when a lot of CNV were called" help="" /> 163 <param argument="--no-gene-labels" type="boolean" checked="false" truevalue="--no-gene-labels" falsevalue="" label="Disable gene_name labels on plot useful when a lot of CNV were called" help="" />
164 </xml> 164 </xml>
165 <xml name="heatmap_optional"> 165 <xml name="heatmap_optional">
166 <param argument="--by-bin" type="boolean" checked="false" truevalue="--by-bin" falsevalue="" label="Plot data x-coordinates by bin indices instead of genomic coordinates" help="" /> 166 <param argument="--by-bin" type="boolean" checked="false" truevalue="--by-bin" falsevalue="" label="Plot data x-coordinates by bin indices instead of genomic coordinates" help="" />
167 <param argument="--chromosome" optional="true" type="text" label="Chromosome range" value="" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" /> 167 <param argument="--chromosome" type="text" label="Chromosome range" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" />
168 <param argument="--desaturate" type="boolean" checked="false" truevalue="--desaturate" falsevalue="" label="Tweak color saturation to focus on significant changes" help="" /> 168 <param argument="--desaturate" type="boolean" checked="false" truevalue="--desaturate" falsevalue="" label="Tweak color saturation to focus on significant changes" help="" />
169 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" /> 169 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
170 <param argument="--no-shift-xy" type="boolean" checked="false" truevalue="--no-shift-xy" falsevalue="" label="Don't adjust the X and Y chromosomes according to sample sex" help="" /> 170 <param argument="--no-shift-xy" type="boolean" checked="false" truevalue="--no-shift-xy" falsevalue="" label="Don't adjust the X and Y chromosomes according to sample sex" help="" />
171 <param argument="--vertical" type="boolean" checked="false" truevalue="--vertical" falsevalue="" label="Plot heatmap with samples as X-axis instead of Y-axis" help="" /> 171 <param argument="--vertical" type="boolean" checked="false" truevalue="--vertical" falsevalue="" label="Plot heatmap with samples as X-axis instead of Y-axis" help="" />
172 <param argument="--delimit-samples" type="boolean" checked="false" truevalue="--delimit-samples" falsevalue="" label="Add an horizontal delimitation line between each sample" help="" /> 172 <param argument="--delimit-samples" type="boolean" checked="false" truevalue="--delimit-samples" falsevalue="" label="Add an horizontal delimitation line between each sample" help="" />
173 <param argument="--title" optional="true" type="text" label="Plot title" value="" help="" /> 173 <param argument="--title" type="text" label="Plot title" help="" />
174 </xml> 174 </xml>
175 <xml name="reference_optional"> 175 <xml name="reference_optional">
176 <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Calculate and store summary stats for clustered subsets of the normal samples with similar coverage profiles" help="" /> 176 <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Calculate and store summary stats for clustered subsets of the normal samples with similar coverage profiles" help="" />
177 <param argument="--min-cluster-size" optional="true" type="integer" label="Minimum cluster size to keep in reference profiles" min="1" value="4" help="" /> 177 <param argument="--min-cluster-size" optional="true" type="integer" label="Minimum cluster size to keep in reference profiles" min="1" value="4" help="" />
178 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Create a male reference" help="shift female samples' chrX log-coverage by -1, so the reference chrX average is -1. Otherwise, shift male samples' chrX by +1, so the reference chrX average is 0" /> 178 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Create a male reference" help="shift female samples' chrX log-coverage by -1, so the reference chrX average is -1. Otherwise, shift male samples' chrX by +1, so the reference chrX average is 0" />
185 <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" /> 185 <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
186 <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="skip edge-effect correction" help="" /> 186 <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="skip edge-effect correction" help="" />
187 <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label="skip repeat master correction" help="" /> 187 <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label="skip repeat master correction" help="" />
188 </xml> 188 </xml>
189 <xml name="scatter_optional"> 189 <xml name="scatter_optional">
190 <param argument="--segment" optional="true" type="data" format="tabular" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" /> 190 <param argument="--segment" optional="true" type="data" format="cns,cnr" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" />
191 <param argument="--chromosome" optional="true" type="text" label="Chromosome range" value="" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" /> 191 <param argument="--chromosome" type="text" label="Chromosome range" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" />
192 <param argument="--gene" optional="true" type="text" label="Name of gene or genes comma-separated to display" value="" help="" /> 192 <param argument="--gene" type="text" label="Name of gene or genes comma-separated to display" help="" />
193 <param argument="--range-list" optional="true" type="data" format="bed" label="Range list" help="File listing the chromosomal ranges to display, as BED"/> 193 <param argument="--range-list" optional="true" type="data" format="bed" label="Range list" help="File listing the chromosomal ranges to display, as BED"/>
194 <param argument="--width" optional="true" type="integer" label="Width" min="1" value="1000000" help="Width of margin to show around the selected genes or small chromosomal region" /> 194 <param argument="--width" optional="true" type="integer" label="Width" min="1" value="1000000" help="Width of margin to show around the selected genes or small chromosomal region" />
195 </xml> 195 </xml>
196 <xml name="scatter_plot"> 196 <xml name="scatter_plot">
197 <param argument="--antitarget-marker" optional="true" type="text" label="Antitarget marker" value="same as targets" help="Plot antitargets using this symbol when plotting in a selected chromosomal region"/> 197 <param argument="--antitarget-marker" type="text" label="Antitarget marker" value="same as targets" help="Plot antitargets using this symbol when plotting in a selected chromosomal region"/>
198 <param argument="--by-bin" type="boolean" checked="false" truevalue="--by-bin" falsevalue="" label="Plot data x-coordinates by bin indices instead of genomic coordinates" help=""/> 198 <param argument="--by-bin" type="boolean" checked="false" truevalue="--by-bin" falsevalue="" label="Plot data x-coordinates by bin indices instead of genomic coordinates" help=""/>
199 <param argument="--segment-color" optional="true" type="text" label="Segment color" value="red" help=""/> 199 <param argument="--segment-color" type="text" label="Segment color" value="red" help=""/>
200 <param argument="--title" optional="true" type="text" label="Plot title" value="" help=""/> 200 <param argument="--title" type="text" label="Plot title" help=""/>
201 <param argument="--trend" type="boolean" checked="false" truevalue="--trend" falsevalue="" label="Draw a smoothed local trendline on the scatter plot" help=""/> 201 <param argument="--trend" type="boolean" checked="false" truevalue="--trend" falsevalue="" label="Draw a smoothed local trendline on the scatter plot" help=""/>
202 <param argument="--y-max" optional="true" type="integer" label="y-axis upper limit" min="1" value="" help=""/> 202 <param argument="--y-max" optional="true" type="integer" label="y-axis upper limit" min="1" value="" help=""/>
203 <param argument="--y-min" optional="true" type="integer" label="y-axis lower limit" min="1" value="" help=""/> 203 <param argument="--y-min" optional="true" type="integer" label="y-axis lower limit" min="1" value="" help=""/>
204 <param argument="--fig-size" optional="true" type="float" label="Width and height of the plot in inches" value="" help="Example 6.4 4.8, the space between the two inputs is important"/> 204 <param argument="--fig-size" optional="true" type="float" label="Width and height of the plot in inches" value="" help="Example 6.4 4.8, the space between the two inputs is important"/>
205 </xml> 205 </xml>
206 <xml name="segment_optional"> 206 <xml name="segment_optional">
207 <param argument="--dataframe" type="text" optional="true" label="Data frame" value="" help="File name to save the raw R dataframe emitted by CBS or Fused Lasso, example dataframe.r"/> 207 <param argument="--dataframe" type="text" label="Data frame" help="File name to save the raw R dataframe emitted by CBS or Fused Lasso, example dataframe.r"/>
208 <param argument="--method" type="select" label="Segmentation method" help=""> 208 <param argument="--method" type="select" label="Segmentation method" help="">
209 <option value="cbs" selected="True">Circular Binary Segmentation CBS method,hybrid CBS</option> 209 <option value="cbs" selected="True">CBS: Circular Binary Segmentation (default, precise)</option>
210 <option value="flasso">Fused lasso, hybrid flasso</option> 210 <option value="flasso">Flasso: Fused Lasso; smoother segments, fewer breakpoints</option>
211 <option value="haar">A pure-Python implementation of HaarSeg, a wavelet-based method. Very fast and performs reasonably well on small panels, but tends to over-segment large datasets., hybrid haar</option> 211 <option value="haar">Haar: Haar wavelet transform; detects abrupt changes</option>
212 <option value="none">simply calculate the weighted mean log2 value of each chromosome arm. Useful for testing or debugging, or as a baseline for benchmarking other methods., hybrid none</option> 212 <option value="none">None: No segmentation; outputs bin-level data as segments</option>
213 <option value="hmm">experimental – a 3-state Hidden Markov Model suitable for most samples. Faster than CBS, and slower but more accurate than Haar. Requires the Python package pomegranate, as do the next two methods., hybrid hmm</option> 213 <option value="hmm">Hmm: Basic Hidden Markov Model (generic use)</option>
214 <option value="hmm-tumor">experimental – a 5-state HMM suitable for finer-grained segmentation of good-quality tumor samples. In particular, this method can detect focal amplifications within a larger-scale, smaller-amplitude copy number gain, or focal deep deletions within a larger-scale hemizygous loss. Training this model takes a bit more CPU time than the simpler hmm method., hybrid hmm-tumor</option> 214 <option value="hmm-tumor">Hmm-tumor: HMM tailored for tumor samples (somatic CNVs)</option>
215 <option value="hmm-germline">experimental – a 3-state HMM with fixed amplitude for the loss, neutral, and gain states corresponding to absolute copy numbers of 1, 2, and 3. Suitable for germline samples and single-cell sequencing of samples with mostly-diploid genomes that are not overly aneuploid., hybrid hmm-germline</option> 215 <option value="hmm-germline">Hmm-germline: HMM for germline (inherited) variants (diploid assumption)</option>
216 </param> 216 </param>
217 <param argument="--threshold" optional="true" type="integer" label="Significance threshold" min="1" help="To accept breakpoints during segmentation. For HMM methods, this is the smoothing window size"/> 217 <param argument="--threshold" optional="true" type="integer" label="Significance threshold" min="1" help="To accept breakpoints during segmentation. For HMM methods, this is the smoothing window size"/>
218 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples"/> 218 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples"/>
219 <param argument="--drop-outliers" optional="true" type="integer" label="Drop outliers" min="1" value="10" help=""/> 219 <param argument="--drop-outliers" optional="true" type="integer" label="Drop outliers" min="1" value="10" help=""/>
220 <param argument="--smooth-cbs" type="boolean" checked="false" truevalue="--smooth-cbs" falsevalue="" label="Perform an additional smoothing before CBS segmentations" help=""/> 220 <param argument="--smooth-cbs" type="boolean" checked="false" truevalue="--smooth-cbs" falsevalue="" label="Perform an additional smoothing before CBS segmentations" help=""/>