Mercurial > repos > iuc > cnvkit_call

annotate call.xml @ 5:e570209e97bf 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 11:53:55 +0000
parents b7b790a1cae0
children
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04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_call" name="CNVkit Call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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2 <description>Call copy number variants from segmented log2 ratios</description>
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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3 <macros>
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4 <import>macros.xml</import>
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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5 </macros>
04793bafe25a 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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46f2af94b1bf 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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04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 ln -s '$input_sample_file' ./tumor.cns &&
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #if $additional_SNP_allelic_process.vcf
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 #end if
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 cnvkit.py call
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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15 ./tumor.cns
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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16 #if $advanced_settings.method == "threshold"
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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17 #set $method_val = "threshold"
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 --method '$method_val'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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19 #else
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20 --method '$advanced_settings.method'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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21 #end if
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22 #if $advanced_settings.center == "median"
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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23 #set $center_val = "median"
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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24 --center '$center_val'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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25 #else
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26 --center '$advanced_settings.center'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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27 #end if
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 #if str($advanced_settings.thresholds)
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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29 --thresholds'$advanced_settings.thresholds'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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30 #end if
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 #if str($advanced_settings.center_at)
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32 --center-at '$advanced_settings.center_at'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 #end if
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34 #if str($advanced_settings.add_filter.Filter) == "yes":
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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35 #if '$advanced_settings.add_filter.filter' == "ampdel"
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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36 #set $filter_val = "ampdel"
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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37 --filter '$filter_val'
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38 #else
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39 --filter '$advanced_settings.add_filter.filter'
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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40 #end if
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41 #end if
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42 #if str($advanced_settings.ploidy)
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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43 --ploidy $advanced_settings.ploidy
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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44 #end if
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45 #if str($advanced_settings.purity)
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46 --purity $advanced_settings.purity
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47 #end if
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48 $advanced_settings.drop_low_coverage
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49 #if str($advanced_settings.Sample_sex.sex) == "yes":
04793bafe25a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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50 #if '$advanced_settings.Sample_sex.sample_sex' == "Male"
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51 #set $sample_sex_val = "Male"
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52 --sample-sex '$segment_method_val'
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53 #else
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54 --sample-sex '$advanced_settings.Sample_sex.sample_sex'
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55 #end if
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56 #end if
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57 $advanced_settings.male_reference
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58 #if $additional_SNP_allelic_process.vcf
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59 --vcf ./vcf_file.vcf
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60 #end if
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61 #if $additional_SNP_allelic_process.sample_id
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62 --sample-id '$additional_SNP_allelic_process.sample_id'
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63 #end if
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64 #if $additional_SNP_allelic_process.normal_id
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65 --normal-id '$additional_SNP_allelic_process.normal_id'
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66 #end if
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67 #if str($additional_SNP_allelic_process.min_variant_depth)
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68 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
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69 #end if
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70 #if str($additional_SNP_allelic_process.zygosity_freq)
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71 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
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72 #end if
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73 ]]></command>
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74 <inputs>
5
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75 <param name="input_sample_file" type="data" format="cns" label="CN segmentation calls cns file" help="" />
0
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76 <section name="additional_SNP_allelic_process" title="additional SNP b_allele frequencies process" expanded="false">
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77 <expand macro="additionally_SNP_process" />
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78 </section>
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79 <section name="advanced_settings" title="Advanced settings" expanded="false">
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80 <expand macro="call_optional" />
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81 <expand macro="sample_sex_condition" />
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82 <conditional name="add_filter">
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83 <param name="Filter" type="select" label="Add filters" help="">
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84 <option value="yes">Add filters</option>
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85 <option value="no" selected="True">don't add filters</option>
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86 </param>
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87 <when value="yes">
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88 <expand macro="filter" />
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89 </when>
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90 <when value="no">
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91 </when>
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92 </conditional>
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93 </section>
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94 </inputs>
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95 <outputs>
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96 <data name="out_sample_Bintest" format="cns" 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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97 </outputs>
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98 <tests>
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99 <test expect_num_outputs="1">
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100 <param name="input_sample_file" ftype="cns" value="tumor.cns" />
3
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101 <section name="additional_SNP_allelic_process">
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102 <param name="zygosity_freq" value="0.25" />
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103 <param name="min_variant_depth" value="40" />
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104 </section>
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105 <section name="advanced_settings">
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106 <param name="purity" value="1" />
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107 </section>
0
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108 <output name="out_sample_Bintest">
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109 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
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110 </output>
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111 </test>
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112 <test expect_num_outputs="1">
3
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113 <section name="advanced_settings">
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114 <conditional name="Sample_sex">
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115 <param name="sex" value="yes" />
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116 </conditional>
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117 <param name="purity" value="1" />
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118 </section>
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119 <param name="input_sample_file" ftype="cns" value="tumor.cns" />
3
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120 <section name="additional_SNP_allelic_process">
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121 <param name="min_variant_depth" value="40" />
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122 </section>
0
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123 <output name="out_sample_Bintest">
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124 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
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125 </output>
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126 </test>
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127 </tests>
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128 <help><![CDATA[
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129 Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number using either:
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130 A list of threshold log2 values for each copy number state (-m threshold), or rescaling - for a given known
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131 tumor cell fraction and normal ploidy, then simple rounding to the nearest integer copy number (-m clonal).
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132
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133 The output is Segmented log2 ratios (.cns) file with those columns
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134 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
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135
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136 -----
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137
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138 **Segmented log2 ratios (.cns)**
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139
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140 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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141
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142 .. csv-table::
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143 :header-rows: 0
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144
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145 "chromosome","start, end: Genomic coordinates of the segment"
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146 "gene","Gene(s) overlapping the segment."
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147 "log2","Mean log2 ratio of the segment."
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148 "probes","Mean log2 ratio of the segment."
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149 "depth","Average read depth."
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150 "weight","Reliability weight."
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151 "p_value","Statistical confidence (lower = more significant)."
0
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152 ]]></help>
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153 <expand macro="citations" />
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154 </tool>