Mercurial > repos > iuc > cnvkit_export_nexus_basic

comparison nexus_basic.xml @ 0:eec611d7ef03 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:26:53 +0000
parents
children 6dc05861aaea
comparison
equal deleted inserted replaced
-1:000000000000 0:eec611d7ef03
1 <tool id="cnvkit_export_nexus_basic" name="CNVkit Export Nexus Basics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Convert bin-level log2 ratios to Nexus Copy Number "basic" 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 '$input_segmented_file' ./sample.cnr &&
11 cnvkit.py export nexus-basic
12 ./sample.cnr
13 --output sample.cnv.tsv
14 ]]></command>
15 <inputs>
16 <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
17 </inputs>
18 <outputs>
19 <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" />
20 </outputs>
21 <tests>
22 <test expect_num_outputs="1">
23 <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
24 <output name="CNVs_NexusBasic" file="sample.cnv.tsv" />
25 </test>
26 </tests>
27 <help><![CDATA[
28 This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format,
29 enabling efficient visualisation and analysis of genomic alterations in Nexus software.
30 This conversion facilitates downstream interpretation and integration with other genomic data.
31 ]]></help>
32 <expand macro="citations" />
33 </tool>