Mercurial > repos > iuc > cnvkit_segment

annotate segment.xml @ 5:bdd0e8e05933 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 12:06:19 +0000 (7 days ago)
parents 33be231ce128
children
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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 $additional_SNP_allelic_process.zygosity_freq
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50 #end if
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51 ]]></command>
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52 <inputs>
5
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53 <param name="filename" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
0
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54 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
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55 <expand macro="additionally_SNP_process" />
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56 </section>
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57 <section name="advanced_settings" title="Advanced settings" expanded="false">
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58 <expand macro="segment_optional" />
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59 </section>
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60 </inputs>
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61 <outputs>
5
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62 <data name="out_sample_segment" format="cns" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1">
5
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66 <param name="filename" ftype="cnr" value="tumor.cnr" />
3
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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)
5
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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.
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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90
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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91 .. csv-table::
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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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)"
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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95 "start","Start position of the bin."
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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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)."
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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98 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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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.
bdd0e8e05933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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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>