Mercurial > repos > iuc > cnvkit_export_seg

annotate seg.xml @ 0:4f28bd5479ec 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 16:31:38 +0000
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children 87c01875b634
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4f28bd5479ec 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_seg" name="CNVkit Export SEG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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2 <description>Convert segments to Segment (SEG) format</description>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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3 <macros>
4f28bd5479ec 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>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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5 </macros>
4f28bd5479ec 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"/>
4f28bd5479ec 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"/>
4f28bd5479ec 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"/>
4f28bd5479ec 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[
4f28bd5479ec 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.cns &&
4f28bd5479ec 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 seg
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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12 ./sample.cns
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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13 $advanced_settings.enumerate_chroms
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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14 --output sample.cnv.seg
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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15 ]]></command>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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16 <inputs>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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17 <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" />
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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18 <section name="advanced_settings" title="Advanced settings" expanded="false">
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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19 <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" />
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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20 </section>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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21 </inputs>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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22 <outputs>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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23 <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" />
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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24 </outputs>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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25 <tests>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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26 <test expect_num_outputs="1">
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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27 <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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28 <output name="CNVs_SEG" file="sample.cnv.seg" />
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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29 </test>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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30 </tests>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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31 <help><![CDATA[
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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32 Export the segmented copy number data (from a .cns file) to the standard SEG format.
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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33 ]]></help>
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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34 <expand macro="citations" />
4f28bd5479ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
iuc
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35 </tool>