Mercurial > repos > iuc > cnvkit_segment

comparison macros.xml @ 1:c4a22d0fdba5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:45:41 +0000
parents 9d9a8f230a2f
children e1b32558547b
comparison
equal deleted inserted replaced
0:9d9a8f230a2f 1:c4a22d0fdba5
1 <macros> 1 <macros>
2 <token name="@VERSION_SUFFIX@">0</token> 2 <token name="@VERSION_SUFFIX@">0.1</token>
3 <token name="@TOOL_VERSION@">0.9.10</token> 3 <token name="@TOOL_VERSION@">0.9.10</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="1.0.2">scikit-learn</requirement> 7 <requirement type="package" version="1.0.2">scikit-learn</requirement>
27 </xml> 27 </xml>
28 <xml name="xrefs"> 28 <xml name="xrefs">
29 <xrefs> 29 <xrefs>
30 <xref type="bio.tools">cnvkit</xref> 30 <xref type="bio.tools">cnvkit</xref>
31 </xrefs> 31 </xrefs>
32 </xml>
33 <xml name="creators">
34 <creator>
35 <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
36 <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
37 <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" />
38 <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
39 <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
40 </creator>
41 </xml>
42 <xml name="creators_and_zahra">
43 <creator>
44 <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
45 <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
46 <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" />
47 <person givenName="zahra" familyName="Karimi" url="https://github.com/zahraK20" />
48 <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
49 <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
50 </creator>
32 </xml> 51 </xml>
33 <xml name="shared"> 52 <xml name="shared">
34 <param argument="--method" type="select" label="Select the sequencing method of the input files" help=""> 53 <param argument="--method" type="select" label="Select the sequencing method of the input files" help="">
35 <option value="hybrid" selected="True">hybridization capture </option> 54 <option value="hybrid" selected="True">hybridization capture </option>
36 <option value="amplicon">targeted amplicon sequencing </option> 55 <option value="amplicon">targeted amplicon sequencing </option>
166 <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="" />
167 <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="" />
168 <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="" />
169 </xml> 188 </xml>
170 <xml name="scatter_optional"> 189 <xml name="scatter_optional">
171 <param argument="--segment" optional="true" type="data" format="cns" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" /> 190 <param argument="--segment" optional="true" type="data" format="tabular" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" />
172 <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" optional="true" type="text" label="Chromosome range" value="" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" />
173 <param argument="--gene" optional="true" type="text" label="Name of gene or genes comma-separated to display" value="" help="" /> 192 <param argument="--gene" optional="true" type="text" label="Name of gene or genes comma-separated to display" value="" help="" />
174 <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"/>
175 <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" />
176 </xml> 195 </xml>
211 </when> 230 </when>
212 <when value="no"> 231 <when value="no">
213 </when> 232 </when>
214 </conditional> 233 </conditional>
215 </xml> 234 </xml>
216 <xml name="citations"> 235 <xml name="genemetrics_segmetrics_statistics">
236 <param argument="--mean" type="boolean" checked="true" truevalue="--mean" falsevalue="" label="Mean log2-ratio" help="" />
237 <param argument="--median" type="boolean" checked="false" truevalue="--median" falsevalue="" label="Median" help="" />
238 <param argument="--mode" type="boolean" checked="false" truevalue="--mode" falsevalue="" label="mode" help="peak density of log2 ratios" />
239 <param argument="--ttest" type="boolean" checked="false" truevalue="--ttest" falsevalue="" label="One-sample t-test" help="bin log2 ratios versus 0.0" />
240 <param argument="--stdev" type="boolean" checked="false" truevalue="--stdev" falsevalue="" label="Standard deviation" help="" />
241 <param argument="--sem" type="boolean" checked="false" truevalue="--sem" falsevalue="" label="Standard error of the mean" help="" />
242 <param argument="--mad" type="boolean" checked="false" truevalue="--mad" falsevalue="" label="Median absolute deviation" help="" />
243 <param argument="--mse" type="boolean" checked="false" truevalue="--mse" falsevalue="" label="mean squared error" help="" />
244 <param argument="--iqr" type="boolean" checked="false" truevalue="--iqr" falsevalue="" label="Inter-quartile range" help="" />
245 <param argument="--bivar" type="boolean" checked="false" truevalue="--bivar" falsevalue="" label="Tukeys biweight midvariance" help="" />
246 <param argument="--ci" type="boolean" checked="false" truevalue="--ci" falsevalue="" label="confidence interval" help="" />
247 <param argument="--pi" type="boolean" checked="false" truevalue="--pi" falsevalue="" label="prediction interval" help="" />
248 <param argument="--alpha" type="boolean" checked="false" truevalue="--alpha" falsevalue="" label="alpha" help="" />
249 <param argument="--bootstrap" type="boolean" checked="false" truevalue="--bootstrap" falsevalue="" label="estimate confidence interval" help="number of bootstrp interations" />
250 </xml>
251 <xml name="citations">
217 <citations> 252 <citations>
218 <citation type="doi">10.1371/journal.pcbi.1004873</citation> 253 <citation type="doi">10.1371/journal.pcbi.1004873</citation>
219 </citations> 254 </citations>
220 </xml> 255 </xml>
221 </macros> 256 </macros>