Mercurial > repos > iuc > bcftools_consensus

annotate bcftools_consensus.xml @ 17:c8747136963c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
author iuc
date Sat, 15 Jan 2022 12:46:20 +0000
parents 703d87c2684c
children 99550ee60e65
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
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3 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">consensus</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements">
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10 <expand macro="samtools_requirement"/>
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11 <requirement type="package" version="5.0.1">gawk</requirement>
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12 </expand>
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13 <expand macro="version_command" />
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14 <command detect_errors="aggressive"><![CDATA[
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15 @PREPARE_ENV@
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16 @PREPARE_INPUT_FILE@
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17 #set $section = $reference_source
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18 @PREPARE_FASTA_REF@
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20 bcftools @EXECUTABLE@
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22 @FASTA_REF@
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24 ## Default section
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25 #set $section = $sec_default
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27 ${section.iupac_codes}
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29 #if $section.mask:
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30 --mask '${section.mask}'
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31 #end if
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33 #if $section.select_haplotype:
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34 --haplotype '${section.select_haplotype}'
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35 #end if
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36 @SAMPLE@
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37
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38 #set $section = $sec_restrict
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39 @INCLUDE@
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40 @EXCLUDE@
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41
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42 #if $chain:
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43 --chain '$chain_file'
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44 #end if
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46 ## Primary Input/Outputs
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47 #if str($rename) == "no"
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48 --output '$output_file'
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49 #end if
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50 @INPUT_FILE@
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51 #if str($rename) == "yes":
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52 #set basename=$input_file.element_identifier
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53 | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name="${basename}"} else {name=sprintf("%s-%d","${basename}",i);} print(gensub(/>[^ ]+( ?.*)/, ">" name "\\1", 1)); i=i+1;} else {print}}' > '$output_file'
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54 #end if
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55 ]]>
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56 </command>
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57 <inputs>
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58 <expand macro="macro_input" />
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59 <expand macro="macro_fasta_ref" />
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60 <section name="sec_default" expanded="true" title="Default Options">
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61 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
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62 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes"
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63 help="Output variants in the form of IUPAC ambiguity codes" />
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64 <expand macro="macro_sample" />
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65 <param name="select_haplotype" type="select" optional="true">
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66 <option value="1">1</option>
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67 <option value="2">2</option>
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68 </param>
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69 </section>
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70 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
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71 <param name="rename" type="boolean" truevalue="yes" falsevalue="no" label="Set output FASTA ID from name of VCF" />
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72 <section name="sec_restrict" expanded="false" title="Restrict to">
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73 <expand macro="macro_include" />
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74 <expand macro="macro_exclude" />
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75 </section>
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76 </inputs>
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77 <outputs>
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78 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
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79 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
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80 <filter>chain</filter>
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <expand macro="test_using_reference" ref="consensus.fa" />
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86 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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87 <param name="mask" ftype="tabular" value="consensus.tab" />
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88 <param name="chain" value="True" />
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89 <output name="output_file">
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90 <assert_contents>
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91 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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92 </assert_contents>
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93 </output>
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94 <output name="chain_file">
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95 <assert_contents>
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96 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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97 </assert_contents>
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98 </output>
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99 </test>
9
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100 <test>
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101 <expand macro="test_using_reference" select_from="cached" ref="consensus" />
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102 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
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103 <param name="mask" ftype="tabular" value="consensus.tab" />
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104 <param name="chain" value="True" />
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105 <output name="output_file">
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106 <assert_contents>
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107 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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108 </assert_contents>
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109 </output>
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110 <output name="chain_file">
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111 <assert_contents>
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112 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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113 </assert_contents>
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114 </output>
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115 </test>
12
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116 <test>
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117 <expand macro="test_using_reference" ref="consensus.fa" />
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118 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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119 <param name="mask" ftype="tabular" value="consensus.tab" />
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120 <param name="chain" value="False" />
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121 <param name="rename" value="True" />
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122 <output name="output_file">
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123 <assert_contents>
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124 <has_text text=">consensus.vcf" />
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125 </assert_contents>
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126 <assert_contents>
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127 <has_text text=">consensus.vcf-2" />
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128 </assert_contents>
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129 </output>
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130 </test>
14
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131 <test>
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132 <expand macro="test_using_reference" ref="consensus.fa" />
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133 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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134 <section name="sec_restrict">
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135 <param name="include" value='TYPE="snp"' />
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136 </section>
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137 <output name="output_file">
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138 <assert_contents>
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139 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" />
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140 </assert_contents>
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141 </output>
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142 </test>
0
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143 </tests>
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144 <help><![CDATA[
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145 =====================================
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146 bcftools @EXECUTABLE@ plugin
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147 =====================================
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148
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149
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150 Create consensus sequence by applying VCF variants to a reference fasta file.
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151
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152 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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153
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154 @BCFTOOLS_WIKI@
12
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155
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156 The option to set the new consensus' FASTA ID from the name of the VCF is provided by post-processing
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157 the bcftools consensus output. It is primarily intended for use when the VCF is coming from a list
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158 collection where the elements of the list are named meaningfully (e.g. named after sample names). This
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159 is useful when consensus sequences are being prepared for, for example, feeding a multiple sequence
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160 alignment to a phylogeny program.
0
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161 ]]>
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162 </help>
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163 <expand macro="citations" />
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164 </tool>