Mercurial > repos > iuc > cnvkit_export_cdt
comparison cdt.xml @ 0:5406089c2db7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
| author | iuc |
|---|---|
| date | Mon, 20 Jan 2025 16:40:16 +0000 |
| parents | |
| children | 21a1d65e26ba |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:5406089c2db7 |
|---|---|
| 1 <tool id="cnvkit_export_cdt" name="CNVkit Export CDT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>Convert log2 ratios to Clustered Data Table (CDT)</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 '$input_segmented_file' ./sample.cnr && | |
| 11 cnvkit.py export cdt | |
| 12 ./sample.cnr | |
| 13 --output sample.cnv.cdt | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="CNVs_cdt" format="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" /> | |
| 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_cdt" file="sample.cnv.cdt" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering. | |
| 29 The conversion enables efficient exploration and interpretation of genomic copy number variations. | |
| 30 ]]></help> | |
| 31 <expand macro="citations" /> | |
| 32 </tool> |