Mercurial > repos > iuc > cnvkit_export_bed

annotate bed.xml @ 1:dad30a23fcd6 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 11:48:59 +0000
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b14f1b2f6196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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1 <tool id="cnvkit_export_bed" name="CNVkit Export BED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Converts the Segmented copy ratio data file (*.cns) file into BED file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="creators"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s '$input_segmented_file' ./sample.cns &&
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11 cnvkit.py export bed
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12 ./sample.cns
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13 $advanced_settings.label_genes
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14 #if $advanced_settings.sample_id
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15 --sample-id '$advanced_settings.sample_id'
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16 #end if
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17 #if $advanced_settings.ploidy
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18 --ploidy $advanced_settings.ploidy
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19 #end if
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20 #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
b14f1b2f6196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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21 --sample-sex '$advanced_settings.sample_sex'
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22 #end if
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23 $advanced_settings.male_reference
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24 --output sample.cnv.bed
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25 #if $advanced_settings.diploid_parx_genome
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26 --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
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27 #end if
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28 ]]></command>
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29 <inputs>
1
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30 <param name="input_segmented_file" type="data" format="cns" label="Segmented Copy Ratio Data File (cns file)" help="" />
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31 <section name="advanced_settings" title="Advanced settings" expanded="false">
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32 <param argument="--label-genes" type="boolean" checked="false" truevalue="--label-genes" falsevalue="" label="Label Genes" help="Show gene names in the 4th column of the BED file" />
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33 <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
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34 <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
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35 <expand macro="sample_sex"/>
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36 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Male Reference" help="Assume inputs were normalized to a male reference" />
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37 <param argument="--diploid-parx-genome" type="text" label="Diploid Parx Genome" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
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38 </section>
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39 </inputs>
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40 <outputs>
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41 <data name="CNVs_BED" format="bed" label="${tool.name} on ${on_string}: CNVs BED file" from_work_dir="sample.cnv.bed" />
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42 </outputs>
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43 <tests>
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44 <test expect_num_outputs="1">
1
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45 <param name="input_segmented_file" ftype="cns" value="sample.cns" />
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46 <param name="sample_id" value="SampleID" />
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47 <param name="sample_sex" value="Female" />
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48 <output name="CNVs_BED" file="sample.cnv.bed" />
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49 </test>
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50 </tests>
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51 <help><![CDATA[
1
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53 Export the segmented copy number data (from a .cns file) to BED format.
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54 The resulting BED file describes copy number gains and losses across each segment.
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55 -----
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57 **Segmented log2 ratios (.cns)**
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59 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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61 .. csv-table::
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62 :header-rows: 0
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64 "chromosome","start, end: Genomic coordinates of the segment"
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65 "gene","Gene(s) overlapping the segment."
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66 "log2","Mean log2 ratio of the segment."
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67 "probes","Mean log2 ratio of the segment."
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68 "depth","Average read depth."
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69 "weight","Reliability weight."
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70 "p_value","Statistical confidence (lower = more significant)."
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72
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73 ]]></help>
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74 <expand macro="citations" />
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75 </tool>
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