Mercurial > repos > iuc > cnvkit_export_nexus_basic

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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 11:52:29 +0000
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eec611d7ef03 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_nexus_basic" name="CNVkit Export Nexus Basics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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2 <description>Convert bin-level log2 ratios to Nexus Copy Number "basic" format</description>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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3 <macros>
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4 <import>macros.xml</import>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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5 </macros>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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6 <expand macro="xrefs"/>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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7 <expand macro="creators"/>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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10 ln -s '$input_segmented_file' ./sample.cnr &&
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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11 cnvkit.py export nexus-basic
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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12 ./sample.cnr
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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13 --output sample.cnv.tsv
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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14 ]]></command>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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15 <inputs>
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6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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16 <param name="input_segmented_file" type="data" format="cnr,cns" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
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17 </inputs>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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18 <outputs>
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19 <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" />
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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20 </outputs>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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21 <tests>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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22 <test expect_num_outputs="1">
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23 <param name="input_segmented_file" ftype="cnr" value="sample.cnr" />
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eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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24 <output name="CNVs_NexusBasic" file="sample.cnv.tsv" />
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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25 </test>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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26 </tests>
eec611d7ef03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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27 <help><![CDATA[
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6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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29 This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format,
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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30 enabling efficient visualisation and analysis of genomic alterations in Nexus software.
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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31 This conversion facilitates downstream interpretation and integration with other genomic data.
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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33 -----
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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35 **Bin-level log2 ratios (.cnr)**
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37 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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39 .. csv-table::
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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40 :header-rows: 0
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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42 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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43 "start","Start position of the bin."
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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44 "end","End position of the bin."
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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45 "gene","Gene name(s) overlapping the bin (if applicable)."
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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46 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
6dc05861aaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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47 "depth","Average read depth in the bin."
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48 "weight","Reliability weight of the bin (higher = more reliable)."
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49
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>