Mercurial > repos > iuc > cnvkit_heatmap

comparison heatmap.xml @ 5:41a25bd96ec6 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 12:07:09 +0000
parents 26554a14f841
children
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4:c76ce257611a 5:41a25bd96ec6
41 #if $advanced_settings.title 41 #if $advanced_settings.title
42 --title '$advanced_settings.title' 42 --title '$advanced_settings.title'
43 #end if 43 #end if
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <param name="filenames" multiple="true" type="data" format="tabular" label="CN segmentation calls cns file/s" help="Sample coverages as raw probes cnr or segments cns" /> 46 <param name="filenames" multiple="true" type="data" format="cns" label="CN segmentation calls cns file/s" help="Sample coverages as raw probes cnr or segments cns" />
47 <section name="advanced_settings" title="Advanced settings" expanded="false"> 47 <section name="advanced_settings" title="Advanced settings" expanded="false">
48 <expand macro="heatmap_optional" /> 48 <expand macro="heatmap_optional" />
49 <expand macro="sample_sex_condition" /> 49 <expand macro="sample_sex_condition" />
50 </section> 50 </section>
51 </inputs> 51 </inputs>
52 <outputs> 52 <outputs>
53 <data name="out_heatmap_png" format="png" label="${tool.name} on ${on_string}: Heatmap png file" from_work_dir="sample-heatmap.png" /> 53 <data name="out_heatmap_png" format="png" label="${tool.name} on ${on_string}: Heatmap png file" from_work_dir="sample-heatmap.png" />
54 </outputs> 54 </outputs>
55 <tests> 55 <tests>
56 <test expect_num_outputs="1"> 56 <test expect_num_outputs="1">
57 <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" /> 57 <param name="filenames" ftype="cns" value="tumor.cns,sample.cns" />
58 <section name="advanced_settings"> 58 <section name="advanced_settings">
59 <param name="desaturate" value="1" /> 59 <param name="desaturate" value="1" />
60 </section> 60 </section>
61 <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" > 61 <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
62 <assert_contents><has_size value="9000" delta="5000" /></assert_contents> 62 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
63 </output> 63 </output>
64 </test> 64 </test>
65 <test expect_num_outputs="1"> 65 <test expect_num_outputs="1">
66 <param name="filenames" ftype="tabular" value="tumor.cns,sample.cns" /> 66 <param name="filenames" ftype="cns" value="tumor.cns,sample.cns" />
67 <section name="advanced_settings"> 67 <section name="advanced_settings">
68 <param name="desaturate" value="1" /> 68 <param name="desaturate" value="1" />
69 <conditional name="Sample_sex"> 69 <conditional name="Sample_sex">
70 <param name="sex" value="no" /> 70 <param name="sex" value="no" />
71 </conditional> 71 </conditional>
75 </output> 75 </output>
76 </test> 76 </test>
77 </tests> 77 </tests>
78 <help><![CDATA[ 78 <help><![CDATA[
79 Draw copy number (either bins (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap 79 Draw copy number (either bins (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap
80
81 -----
82
83 **Segmented log2 ratios (.cns)**
84
85 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
86
87 .. csv-table::
88 :header-rows: 0
89
90 "chromosome","start, end: Genomic coordinates of the segment"
91 "gene","Gene(s) overlapping the segment."
92 "log2","Mean log2 ratio of the segment."
93 "probes","Mean log2 ratio of the segment."
94 "depth","Average read depth."
95 "weight","Reliability weight."
96 "p_value","Statistical confidence (lower = more significant)."
97
80 ]]></help> 98 ]]></help>
81 <expand macro="citations" /> 99 <expand macro="citations" />
82 </tool> 100 </tool>