Mercurial > repos > iuc > cnvkit_reference

annotate reference.xml @ 2:0c3db8ec44b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:41:46 +0000
parents 83470ecad188
children
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75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_reference" name="CNVkit Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Compile a copy-number reference from the given files or directory containing normal samples</description>
75eca7985d89 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>
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5 </macros>
75eca7985d89 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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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 #import re
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 #if str($CNV_reference.CNV_reference_availabel) == "yes"
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 #set $names = []
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13 #set $x=1
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14 #for $x, $input in enumerate($CNV_reference.input_cnn_file):
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15 #set $name_base = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
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16 #set $name = $name_base
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17 #silent $names.append( $name )
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 ln -s '$input' ${name}.cnn &&
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19 #end for
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20 #end if
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21 #if str($CNV_reference.CNV_reference_availabel) == "no"
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22 #if $CNV_reference.antitargets
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23 ln -s '$CNV_reference.antitargets' ./antitargets.bed &&
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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24 #end if
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25 ln -s '$CNV_reference.targets' ./targets.bed &&
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26 #end if
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27 #if $CNV_reference.advanced_settings.reference_source.fasta
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28 #if str($CNV_reference.advanced_settings.reference_source.ref_selector) == 'history':
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29 ln -s '$CNV_reference.advanced_settings.reference_source.fasta' ./genome.fa &&
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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30 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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31 #else
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32 ln -s '$CNV_reference.advanced_settings.reference_source.fasta.fields.path' ./genome.fa &&
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 ln -s '${CNV_reference.advanced_settings.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
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34 #end if
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35 #end if
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36 cnvkit.py reference
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37 #if str($CNV_reference.CNV_reference_availabel) == "yes"
75eca7985d89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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38 #for $name in $names:
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39 ${name}.cnn
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40 #end for
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41 #end if
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42 --output ref-tas.cnn
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43 $CNV_reference.advanced_settings.cluster
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44 #if str($CNV_reference.advanced_settings.min_cluster_size)
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45 --min-cluster-size '$CNV_reference.advanced_settings.min_cluster_size'
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46 #end if
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47 #if str($CNV_reference.advanced_settings.Sample_sex.sex) == "yes":
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48 #if '$CNV_reference.advanced_settings.Sample_sex.sample_sex' == "Male"
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49 #set $sample_sex_val = "Male"
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50 --sample-sex '$segment_method_val'
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51 #else
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52 --sample-sex '$CNV_reference.advanced_settings.Sample_sex.sample_sex'
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53 #end if
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54 #end if
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55 $CNV_reference.advanced_settings.male_reference
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56 #if str($CNV_reference.CNV_reference_availabel) == "no"
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57 --targets ./targets.bed
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58 #if $CNV_reference.antitargets
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59 --antitargets ./antitargets.bed
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60 #end if
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61 #end if
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62 $CNV_reference.disable_some_of_the_bias_corrections.no_gc
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63 $CNV_reference.disable_some_of_the_bias_corrections.no_edge
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64 $CNV_reference.disable_some_of_the_bias_corrections.no_rmask
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65 ]]></command>
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66 <inputs>
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67 <conditional name="CNV_reference">
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68 <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file cnn?" help="">
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69 <option value="no" selected="True">Build a new copy number reference file</option>
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70 <option value="yes">Reuse a copy number reference file</option>
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71 </param>
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72 <when value="no">
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73 <expand macro="construct_CNV_ref_with_natural_expected_number" />
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74 <section name="advanced_settings" title="Advanced settings" expanded="false">
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75 <expand macro="reference_interface" />
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76 <expand macro="reference_optional" />
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77 <expand macro="sample_sex_condition" />
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78 </section>
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79 <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
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80 <expand macro="disable_specific_automatic_bias_corrections" />
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81 </section>
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82 </when>
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83 <when value="yes">
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84 <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="Sample Target/antitarget Coverage cnn file" help="" />
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85 <section name="advanced_settings" title="Advanced settings" expanded="false">
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86 <expand macro="reference_interface" />
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87 <expand macro="reference_optional" />
1
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88 <expand macro="sample_sex_condition" />
0
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89 </section>
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90 <section name="disable_some_of_the_bias_corrections" title="Bias corrections settings" expanded="false">
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91 <expand macro="disable_specific_automatic_bias_corrections" />
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92 </section>
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93 </when>
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94 </conditional>
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95 </inputs>
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96 <outputs>
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97 <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
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98 </outputs>
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99 <tests>
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100 <test expect_num_outputs="1">
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101 <conditional name="reference_source">
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102 <param name="ref_selector" value="history"/>
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103 <param name="fasta" ftype="fasta" value="genome.fasta" />
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104 </conditional>
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105 <param name="CNV_reference_availabel" value="yes" />
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106 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
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107 <param name="no_gc" value="1" />
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108 <output name="out_referene_tas" file="ref-tas.cnn" />
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109 </test>
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110 <test expect_num_outputs="1">
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111 <conditional name="reference_source">
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112 <param name="ref_selector" value="cached"/>
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113 <param name="fasta" value="test_buildid"/>
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114 </conditional>
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115 <param name="CNV_reference_availabel" value="yes" />
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116 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
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117 <param name="no_gc" value="1" />
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118 <output name="out_referene_tas" file="ref-tas.cnn" />
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119 </test>
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120 <test expect_num_outputs="1">
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121 <conditional name="reference_source">
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122 <param name="ref_selector" value="cached"/>
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123 <param name="fasta" value="test_buildid"/>
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124 </conditional>
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125 <param name="CNV_reference_availabel" value="yes" />
2
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126 <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
0
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127 <param name="no_gc" value="1" />
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128 <output name="out_referene_tas">
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129 <assert_contents><has_text text="chromosome"/></assert_contents>
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130 </output>
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131 </test>
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132 <test expect_num_outputs="1">
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133 <conditional name="reference_source">
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134 <param name="ref_selector" value="cached"/>
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135 <param name="fasta" value="test_buildid"/>
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136 </conditional>
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137 <param name="CNV_reference_availabel" value="no" />
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138 <param name="targets" ftype="bed" value="capture.target.bed" />
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139 <param name="no_gc" value="1" />
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140 <output name="out_referene_tas">
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141 <assert_contents><has_text text="chromosome"/></assert_contents>
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142 </output>
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143 </test>
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144 <test expect_num_outputs="1">
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145 <conditional name="reference_source">
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146 <param name="ref_selector" value="cached"/>
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147 <param name="fasta" value="test_buildid"/>
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148 </conditional>
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149 <conditional name="Sample_sex">
2
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150 <param name="sex" value="no" />
0
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151 </conditional>
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152 <param name="CNV_reference_availabel" value="no" />
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153 <param name="targets" ftype="bed" value="capture.target.bed" />
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154 <param name="no_gc" value="1" />
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155 <output name="out_referene_tas">
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156 <assert_contents><has_text text="chromosome"/></assert_contents>
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157 </output>
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158 </test>
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159 </tests>
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160 <help><![CDATA[
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161 Compile a copy-number reference from the given files or directory (containing normal samples).
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162 If given a reference genome (-f option), also calculate the GC content and repeat-masked
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163 proportion of each region.
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164
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165 The reference .cnn file output contains those columns
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166 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
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167 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
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168 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
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169
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170 ]]></help>
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171 <expand macro="citations" />
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172 </tool>