Mercurial > repos > iuc > cnvkit_segment

annotate segment.xml @ 4:5051e0f61b47 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 11:56:31 +0000
parents d5b444c208dd
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1 <tool id="cnvkit_segment" name="CNVkit Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Infer copy number segments from the given coverage table</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[
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10 ln -s '$filename' ./tumor.cnr &&
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11 #if $additional_SNP_allelic_process.vcf
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12 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
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13 #end if
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14 #import os
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15 cnvkit.py segment
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16 ./tumor.cnr
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17 --output sample.cns
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18 --processes \${GALAXY_SLOTS:-4}
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19 #if $advanced_settings.dataframe
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20 --dataframe '$advanced_settings.dataframe'
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21 #end if
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22 #if $advanced_settings.method == "cbs"
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23 #set $method_val = "cbs"
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24 --method '$method_val'
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25 #else
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26 --method '$advanced_settings.method'
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27 #end if
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28 #if str($advanced_settings.threshold)
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29 --threshold $advanced_settings.threshold
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30 #end if
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31 $advanced_settings.drop_low_coverage
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32 #if str($advanced_settings.drop_outliers)
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33 --drop-outliers $advanced_settings.drop_outliers
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34 #end if
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35 $advanced_settings.smooth_cbs
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36 #if $additional_SNP_allelic_process.vcf
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37 --vcf ./vcf_file.vcf
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38 #end if
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39 #if $additional_SNP_allelic_process.sample_id
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40 --sample-id '$additional_SNP_allelic_process.sample_id'
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41 #end if
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42 #if $additional_SNP_allelic_process.normal_id
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43 --normal-id '$additional_SNP_allelic_process.normal_id'
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44 #end if
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45 #if str($additional_SNP_allelic_process.min_variant_depth)
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46 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
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47 #end if
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48 #if str($additional_SNP_allelic_process.zygosity_freq)
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49 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
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50 #end if
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51 ]]></command>
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52 <inputs>
4
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53 <param name="filename" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
0
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54 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
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55 <expand macro="additionally_SNP_process" />
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56 </section>
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57 <section name="advanced_settings" title="Advanced settings" expanded="false">
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58 <expand macro="segment_optional" />
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59 </section>
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60 </inputs>
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61 <outputs>
4
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62 <data name="out_sample_segment" format="cns" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
0
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1">
4
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66 <param name="filename" ftype="cnr" value="tumor.cnr" />
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67 <section name="advanced_settings">
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68 <param name="method" value="hmm" />
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69 <param name="threshold" value="2" />
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70 <param name="drop_outliers" value="2" />
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71 <param name="drop_low_coverage" value="1" />
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72 </section>
0
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73 <output name="out_sample_segment">
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74 <assert_contents><has_text text="chromosome"/></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 Infer copy number segments from the given coverage table. Segmentation runs independently on
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80 each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
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81
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82 Segmented log2 ratios (.cns) output file contains those columns
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83 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
4
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84
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85 -----
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86
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87 **Bin-level log2 ratios (.cnr)**
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88
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89 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
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90
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91 .. csv-table::
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92 :header-rows: 0
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93
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94 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
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95 "start","Start position of the bin."
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96 "end","End position of the bin."
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97 "gene","Gene name(s) overlapping the bin (if applicable)."
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98 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
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99 "depth","Average read depth in the bin."
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100 "weight","Reliability weight of the bin (higher = more reliable)."
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101
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102 -----
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103
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104 **Segmented log2 ratios (.cns)**
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105
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106 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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107
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108 .. csv-table::
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109 :header-rows: 0
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110
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111 "chromosome","start, end: Genomic coordinates of the segment"
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112 "gene","Gene(s) overlapping the segment."
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113 "log2","Mean log2 ratio of the segment."
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114 "probes","Mean log2 ratio of the segment."
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115 "depth","Average read depth."
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116 "weight","Reliability weight."
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117 "p_value","Statistical confidence (lower = more significant)."
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118
0
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119 ]]></help>
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120 <expand macro="citations" />
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121 </tool>