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 12:02:03 +0000
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5f3e6356a8de 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">
5f3e6356a8de 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>
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3 <macros>
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4 <import>macros.xml</import>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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5 </macros>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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6 <expand macro="xrefs"/>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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7 <expand macro="creators"/>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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8 <expand macro="requirements"/>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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9 <command detect_errors="exit_code"><![CDATA[
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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10 ln -s '$input_segmented_file' ./sample.cnr &&
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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11 cnvkit.py export nexus-basic
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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12 ./sample.cnr
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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13 --output sample.cnv.tsv
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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14 ]]></command>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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15 <inputs>
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16 <param name="input_segmented_file" type="data" format="cnr,cns" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
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17 </inputs>
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18 <outputs>
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19 <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" />
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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20 </outputs>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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21 <tests>
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22 <test expect_num_outputs="1">
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b1e27c68c067 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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23 <param name="input_segmented_file" ftype="cnr" value="sample.cnr" />
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5f3e6356a8de 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" />
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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25 </test>
5f3e6356a8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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26 </tests>
5f3e6356a8de 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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29 This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format,
b1e27c68c067 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.
b1e27c68c067 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.
b1e27c68c067 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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33 -----
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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.
b1e27c68c067 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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39 .. csv-table::
b1e27c68c067 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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40 :header-rows: 0
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42 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
b1e27c68c067 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."
b1e27c68c067 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."
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45 "gene","Gene name(s) overlapping the bin (if applicable)."
b1e27c68c067 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)."
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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
0
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>