Mercurial > repos > iuc > cnvkit_heatmap

annotate heatmap.xml @ 4:7b9178a6bffc 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 11:57:15 +0000
parents 10ff342adcbe
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5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_heatmap" name="CNVkit Heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Plot copy number for multiple samples as a heatmap</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="creators"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 #import re
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #set $names = []
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12 #set $x=1
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13 #for $x, $file in enumerate($filenames):
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 #set $name_base = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
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15 #set $name = $name_base
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16 #silent $names.append( $name )
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17 ln -s '$file' ${name}.cns &&
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 #end for
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19 cnvkit.py heatmap
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20 #for $name in $names:
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21 ${name}.cns
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22 #end for
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23 --output sample-heatmap.png
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24 $advanced_settings.by_bin
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25 #if $advanced_settings.chromosome
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26 --chromosome '$advanced_settings.chromosome'
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27 #end if
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28 $advanced_settings.desaturate
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29 $advanced_settings.male_reference
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30 #if str($advanced_settings.Sample_sex.sex) == "yes":
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31 #if '$advanced_settings.Sample_sex.sample_sex' == "Male"
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32 #set $sample_sex_val = "Male"
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 --sample-sex '$segment_method_val'
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34 #else
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35 --sample-sex '$advanced_settings.Sample_sex.sample_sex'
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36 #end if
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37 #end if
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38 $advanced_settings.no_shift_xy
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39 $advanced_settings.vertical
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40 $advanced_settings.delimit_samples
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41 #if $advanced_settings.title
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42 --title '$advanced_settings.title'
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43 #end if
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44 ]]></command>
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45 <inputs>
4
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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" />
0
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47 <section name="advanced_settings" title="Advanced settings" expanded="false">
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48 <expand macro="heatmap_optional" />
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49 <expand macro="sample_sex_condition" />
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50 </section>
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51 </inputs>
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52 <outputs>
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53 <data name="out_heatmap_png" format="png" label="${tool.name} on ${on_string}: Heatmap png file" from_work_dir="sample-heatmap.png" />
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54 </outputs>
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55 <tests>
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56 <test expect_num_outputs="1">
4
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57 <param name="filenames" ftype="cns" value="tumor.cns,sample.cns" />
2
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58 <section name="advanced_settings">
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59 <param name="desaturate" value="1" />
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60 </section>
0
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61 <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
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62 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
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63 </output>
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64 </test>
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65 <test expect_num_outputs="1">
4
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66 <param name="filenames" ftype="cns" value="tumor.cns,sample.cns" />
2
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67 <section name="advanced_settings">
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68 <param name="desaturate" value="1" />
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69 <conditional name="Sample_sex">
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70 <param name="sex" value="no" />
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71 </conditional>
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72 </section>
0
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73 <output name="out_heatmap_png" file="sample-heatmap.png" ftype="png" compare="sim_size" >
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74 <assert_contents><has_size value="9000" delta="5000" /></assert_contents>
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75 </output>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 Draw copy number (either bins (.cnn, .cnr) or segments (.cns)) for multiple samples as a heatmap
4
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80
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81 -----
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82
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83 **Segmented log2 ratios (.cns)**
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84
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85 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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86
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87 .. csv-table::
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88 :header-rows: 0
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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89
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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90 "chromosome","start, end: Genomic coordinates of the segment"
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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91 "gene","Gene(s) overlapping the segment."
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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92 "log2","Mean log2 ratio of the segment."
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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93 "probes","Mean log2 ratio of the segment."
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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94 "depth","Average read depth."
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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95 "weight","Reliability weight."
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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96 "p_value","Statistical confidence (lower = more significant)."
7b9178a6bffc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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97
0
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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98 ]]></help>
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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99 <expand macro="citations" />
5cadfed93e73 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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100 </tool>