Mercurial > repos > iuc > cnvkit_batch

annotate batch.xml @ 2:0d371963d4b9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5
author iuc
date Fri, 13 Dec 2024 23:53:57 +0000
parents 0c60bd0f4de6
children 004311c34527
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840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_batch" name="CNVkit Batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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2 <description>Run the CNVkit pipeline on one or more BAM files</description>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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3 <macros>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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4 <import>macros.xml</import>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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5 </macros>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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6 <expand macro="xrefs"/>
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0c60bd0f4de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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7 <expand macro="creators"/>
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840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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8 <expand macro="requirements"/>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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9 <command detect_errors="exit_code"><![CDATA[
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 ln -s '$CNV_reference.input_sample_file' ./tumor.bam &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 #if str($CNV_reference.CNV_reference_availabel) == "yes":
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 ln -s '$CNV_reference.reference' ./reference.cnn &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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15 #if str($CNV_reference.CNV_reference_availabel) == "no":
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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16 ln -s '$CNV_reference.normal' ./normal.bam &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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17 ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 #if $CNV_reference.advanced_settings.antitargets
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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19 ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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20 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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21 #if $CNV_reference.advanced_settings.annotate
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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22 ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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23 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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24 #if $CNV_reference.advanced_settings.access
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25 ln -s '$CNV_reference.advanced_settings.access' ./access.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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26 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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27 ln -s '$CNV_reference.targets' ./capture.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 #if str($CNV_reference.reference_source.ref_selector) == 'history':
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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29 ln -s '$CNV_reference.reference_source.fasta' ./genome.fa &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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30 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 #else
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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32 ln -s '$CNV_reference.reference_source.fasta.fields.path' ./genome.fa &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 ln -s '${CNV_reference.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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34 #end if
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35 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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36 #import os
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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37 cnvkit.py batch
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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38 ./tumor.bam
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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39 #if str($CNV_reference.CNV_reference_availabel) == "no":
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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40 --normal ./normal.bam
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41 --targets ./capture.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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42 --fasta ./genome.fa
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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43 #if $CNV_reference.advanced_settings.antitargets
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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44 --antitargets ./antitargets.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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45 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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46 #if $CNV_reference.advanced_settings.annotate
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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47 --annotate ./annotate.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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48 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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49 #if $CNV_reference.advanced_settings.access
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50 --access ./access.bed
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51 #end if
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52 #end if
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53 #if str($CNV_reference.CNV_reference_availabel) == "yes":
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54 --reference ./reference.cnn
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55 #end if
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56 $output_section.scatter
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57 $output_section.diagram
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58 --processes \${GALAXY_SLOTS:-4}
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59 #if $CNV_reference.advanced_settings.method == "hybrid"
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60 #set $method_val = "hybrid"
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61 --method '$method_val'
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62 #else
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63 --method '$CNV_reference.advanced_settings.method'
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64 #end if
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65
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66 #if $CNV_reference.advanced_settings.segment_method == "cbs"
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67 #set $segment_method_val = "cbs"
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68 --segment-method '$segment_method_val'
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69 #else
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70 --segment-method '$CNV_reference.advanced_settings.segment_method'
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71 #end if
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72 $CNV_reference.advanced_settings.male_reference
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73 $CNV_reference.advanced_settings.countreads
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74 $CNV_reference.advanced_settings.drop_low_coverage
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75
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76 #if str($CNV_reference.CNV_reference_availabel) == "no":
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77 $CNV_reference.advanced_settings.short_names
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78 #if str($CNV_reference.advanced_settings.target_avg_size)
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79 --target-avg-size $CNV_reference.advanced_settings.target_avg_size
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80 #end if
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81 #if str($CNV_reference.advanced_settings.antitarget_avg_size)
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82 --antitarget-avg-size $CNV_reference.advanced_settings.antitarget_avg_size
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83 #end if
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84 #if str($CNV_reference.advanced_settings.antitarget_min_size)
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85 --antitarget-min-size $CNV_reference.advanced_settings.antitarget_min_size
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86 #end if
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87 $CNV_reference.advanced_settings.cluster
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88 #end if
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89 ]]></command>
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90 <inputs>
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91 <conditional name="CNV_reference">
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92 <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file (.cnn)?" help="">
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93 <option value="no" selected="True">Build a new copy number reference file</option>
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94 <option value="yes">Reuse a copy number reference file</option>
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95 </param>
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96 <when value="no">
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97 <expand macro="create_CNV_reference_file" />
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98 <expand macro="reference_interface" />
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99 <section name="advanced_settings" title="Advanced settings" expanded="false">
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100 <expand macro="advanced_no_reference" />
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101 <expand macro="shared" />
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102 </section>
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103 </when>
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104 <when value="yes">
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105 <expand macro="reuse_an_existing_cnv_reference_file" />
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106 <section name="advanced_settings" title="Advanced settings" expanded="false">
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107 <expand macro="shared" />
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108 </section>
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109 </when>
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110 </conditional>
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111 <expand macro="output_section" />
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112 </inputs>
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113 <outputs>
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114 <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
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115 <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
1
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116 <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
0
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117 <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
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118 <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
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119 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
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120 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
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121 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
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122 </data>
1
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123 <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
0
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124 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
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125 </data>
1
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126 <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
0
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127 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
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128 </data>
1
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129 <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
0
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130 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
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131 </data>
1
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132 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
0
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133 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
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134 </data>
1
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135 <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
0
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136 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
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137 </data>
1
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138 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
0
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139 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
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140 </data>
1
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141 <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Sample Diagram" from_work_dir="tumor-diagram.pdf">
0
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142 <filter>output_section['diagram']</filter>
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143 </data>
1
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144 <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Sample Scatter pdf plot " from_work_dir="tumor-scatter.png">
0
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145 <filter>output_section['scatter']</filter>
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146 </data>
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147 </outputs>
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148 <tests>
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149 <test expect_num_outputs="13">
2
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150 <conditional name="CNV_reference">
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151 <conditional name="reference_source">
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152 <param name="ref_selector" value="history"/>
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153 <param name="fasta" ftype="fasta" value="genome.fasta" />
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154 </conditional>
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155 <param name="CNV_reference_availabel" value="no" />
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156 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
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157 <param name="normal" ftype="bam" value="normal.bam" />
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158 <param name="targets" ftype="bed" value="capture.bed" />
0
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159 </conditional>
2
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160 <section name="output_section">
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161 <param name="scatter" value="1"/>
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162 <param name="diagram" value="1"/>
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163 </section>
0
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164 <output name="out_sample_bintest" file="tumor.bintest.cns" />
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165 <output name="out_sample_antitargetcoverage">
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166 <assert_contents><has_text text="chromosome"/></assert_contents>
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167 </output>
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168 <output name="out_sample_call">
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169 <assert_contents><has_text text="chromosome"/></assert_contents>
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170 </output>
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171 <output name="out_sample_cnr">
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172 <assert_contents><has_text text="chromosome"/></assert_contents>
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173 </output>
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174 <output name="out_sample_targetcoverage_cnn">
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175 <assert_contents><has_text text="chromosome"/></assert_contents>
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176 </output>
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177 <output name="out_sample_cns">
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178 <assert_contents><has_text text="chromosome"/></assert_contents>
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179 </output>
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180 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
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181 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
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182 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
2
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183 <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
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184 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
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185 </output>
0
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186 <output name="out_capture_target">
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187 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
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188 </output>
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189 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
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190 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
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191 </output>
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192 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
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193 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
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194 </output>
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195 </test>
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196 <test expect_num_outputs="13">
2
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197 <conditional name="CNV_reference">
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198 <conditional name="reference_source">
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199 <param name="ref_selector" value="cached"/>
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200 <param name="fasta" value="test_buildid"/>
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201 </conditional>
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202 <param name="CNV_reference_availabel" value="no" />
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203 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
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204 <param name="normal" ftype="bam" value="normal.bam" />
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205 <param name="targets" ftype="bed" value="capture.bed" />
0
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206 </conditional>
2
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207 <section name="output_section">
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208 <param name="scatter" value="1"/>
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209 <param name="diagram" value="1"/>
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210 </section>
0
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211 <output name="out_sample_bintest" file="tumor.bintest.cns" />
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212 <output name="out_sample_antitargetcoverage">
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213 <assert_contents><has_text text="chromosome"/></assert_contents>
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214 </output>
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215 <output name="out_sample_call">
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216 <assert_contents><has_text text="chromosome"/></assert_contents>
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217 </output>
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218 <output name="out_sample_cnr">
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219 <assert_contents><has_text text="chromosome"/></assert_contents>
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220 </output>
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221 <output name="out_sample_targetcoverage_cnn">
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222 <assert_contents><has_text text="chromosome"/></assert_contents>
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223 </output>
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224 <output name="out_sample_cns">
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225 <assert_contents><has_text text="chromosome"/></assert_contents>
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226 </output>
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227 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
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228 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
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229 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
2
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230 <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
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231 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
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232 </output>
0
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233 <output name="out_capture_target">
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234 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
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235 </output>
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236 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
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237 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
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238 </output>
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239 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
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240 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
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241 </output>
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242 </test>
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243 <test expect_num_outputs="10">
2
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244 <conditional name="CNV_reference">
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245 <param name="CNV_reference_availabel" value="yes" />
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246 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
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247 <param name="reference" ftype="tabular" value="reference.cnn" />
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248 </conditional>
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249 <section name="output_section">
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250 <param name="scatter" value="1"/>
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251 <param name="diagram" value="1"/>
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252 </section>
0
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253 <output name="out_sample_bintest" file="tumor.bintest.cns" />
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254 <output name="out_sample_antitargetcoverage">
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255 <assert_contents><has_text text="chromosome"/></assert_contents>
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256 </output>
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257 <output name="out_sample_call">
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258 <assert_contents><has_text text="chromosome"/></assert_contents>
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259 </output>
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260 <output name="out_sample_cnr">
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261 <assert_contents><has_text text="chromosome"/></assert_contents>
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262 </output>
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263 <output name="out_sample_targetcoverage_cnn">
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264 <assert_contents><has_text text="chromosome"/></assert_contents>
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265 </output>
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266 <output name="out_sample_cns">
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267 <assert_contents><has_text text="chromosome"/></assert_contents>
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268 </output>
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269 <output name="out_reference_target_bed" file="reference.target-tmp.bed" />
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270 <output name="out_reference_antitarget_bed" file="reference.antitarget-tmp.bed" />
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271 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
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272 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
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273 </output>
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274 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
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275 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
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276 </output>
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277 </test>
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278 </tests>
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279 <help><![CDATA[
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280 CNVkit pipeline for copy-number changes and allelic imbalances detection
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281 cnn, cnr and cns are tabuler files extintions:
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282
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283 The reference .cnn file has the columns:
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284 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
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285 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
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286 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
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287
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288 Target and antitarget bin-level coverages (.cnn)
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289 chromosome, Start, end, gene, log2 and depth
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290
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291 Bin-level log2 ratios (.cnr)
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292 chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight)
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293
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294 Segmented log2 ratios (.cns)
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295 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
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296
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297
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298 ]]></help>
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299 <expand macro="citations" />
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300 </tool>