Mercurial > repos > iuc > cnvkit_export_seg

comparison seg.xml @ 1:87c01875b634 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:56:09 +0000
parents 4f28bd5479ec
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0:4f28bd5479ec 1:87c01875b634
12 ./sample.cns 12 ./sample.cns
13 $advanced_settings.enumerate_chroms 13 $advanced_settings.enumerate_chroms
14 --output sample.cnv.seg 14 --output sample.cnv.seg
15 ]]></command> 15 ]]></command>
16 <inputs> 16 <inputs>
17 <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" /> 17 <param name="input_segmented_file" type="data" format="cns" label="Segmented copy ratio data file (cns file)" help="" />
18 <section name="advanced_settings" title="Advanced settings" expanded="false"> 18 <section name="advanced_settings" title="Advanced settings" expanded="false">
19 <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" /> 19 <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" />
20 </section> 20 </section>
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" /> 23 <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" />
24 </outputs> 24 </outputs>
25 <tests> 25 <tests>
26 <test expect_num_outputs="1"> 26 <test expect_num_outputs="1">
27 <param name="input_segmented_file" ftype="tabular" value="sample.cns" /> 27 <param name="input_segmented_file" ftype="cns" value="sample.cns" />
28 <output name="CNVs_SEG" file="sample.cnv.seg" /> 28 <output name="CNVs_SEG" file="sample.cnv.seg" />
29 </test> 29 </test>
30 </tests> 30 </tests>
31 <help><![CDATA[ 31 <help><![CDATA[
32 Export the segmented copy number data (from a .cns file) to the standard SEG format. 32 Export the segmented copy number data (from a .cns file) to the standard SEG format.
33
34 -----
35
36 **Segmented log2 ratios (.cns)**
37
38 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
39
40 .. csv-table::
41 :header-rows: 0
42
43 "chromosome","start, end: Genomic coordinates of the segment"
44 "gene","Gene(s) overlapping the segment."
45 "log2","Mean log2 ratio of the segment."
46 "probes","Mean log2 ratio of the segment."
47 "depth","Average read depth."
48 "weight","Reliability weight."
49 "p_value","Statistical confidence (lower = more significant)."
50
33 ]]></help> 51 ]]></help>
34 <expand macro="citations" /> 52 <expand macro="citations" />
35 </tool> 53 </tool>