Mercurial > repos > iuc > cnvkit_export_seg

comparison 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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1 <tool id="cnvkit_export_seg" name="CNVkit Export SEG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Convert segments to Segment (SEG) format</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_segmented_file' ./sample.cns &&
11 cnvkit.py export seg
12 ./sample.cns
13 $advanced_settings.enumerate_chroms
14 --output sample.cnv.seg
15 ]]></command>
16 <inputs>
17 <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" />
18 <section name="advanced_settings" title="Advanced settings" expanded="false">
19 <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" />
20 </section>
21 </inputs>
22 <outputs>
23 <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" />
24 </outputs>
25 <tests>
26 <test expect_num_outputs="1">
27 <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
28 <output name="CNVs_SEG" file="sample.cnv.seg" />
29 </test>
30 </tests>
31 <help><![CDATA[
32 Export the segmented copy number data (from a .cns file) to the standard SEG format.
33 ]]></help>
34 <expand macro="citations" />
35 </tool>