Mercurial > repos > iuc > cnvkit_export_cdt

annotate cdt.xml @ 0:8834638e3248 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:29:29 +0000
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8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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1 <tool id="cnvkit_export_cdt" name="CNVkit Export CDT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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2 <description>Convert log2 ratios to Clustered Data Table (CDT)</description>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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3 <macros>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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4 <import>macros.xml</import>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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5 </macros>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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6 <expand macro="xrefs"/>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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7 <expand macro="creators"/>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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8 <expand macro="requirements"/>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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9 <command detect_errors="exit_code"><![CDATA[
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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10 ln -s '$input_segmented_file' ./sample.cnr &&
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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11 cnvkit.py export cdt
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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12 ./sample.cnr
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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13 --output sample.cnv.cdt
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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14 ]]></command>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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15 <inputs>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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16 <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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17 </inputs>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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18 <outputs>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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19 <data name="CNVs_cdt" format="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" />
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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20 </outputs>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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21 <tests>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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22 <test expect_num_outputs="1">
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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23 <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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24 <output name="CNVs_cdt" file="sample.cnv.cdt" />
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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25 </test>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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26 </tests>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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27 <help><![CDATA[
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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28 This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering.
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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29 The conversion enables efficient exploration and interpretation of genomic copy number variations.
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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30 ]]></help>
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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31 <expand macro="citations" />
8834638e3248 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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32 </tool>