Mercurial > repos > jjohnson > bcftools_reheader

annotate bcftools_reheader.xml @ 0:4a6d130d8eb8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:52:30 -0400
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children c547813e234e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4a6d130d8eb8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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="@VERSION@.0">
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3 <description>Modify header of VCF/BCF files, change sample names</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">reheader</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILE@
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13 bcftools @EXECUTABLE@
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14
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15 #set $section = $sec_default
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16
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17 #if $section.header:
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18 --header "${section.header}"
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19 #end if
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20
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21 #if $section.rename_samples.samples_src == 'history':
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22 --samples "${section.rename_samples.sample_file}"
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23 #elif $section.rename_samples.samples_src == 'entry':
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24 --samples "${entered_sample_file}"
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25 #end if
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26
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27 ## Primary Input/Outputs
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28 @INPUT_FILE@
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29 | bcftools view
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30 @OUTPUT_TYPE@
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31 > "$output_file"
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32 ]]>
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33 </command>
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34 <configfiles>
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35 <configfile name="entered_sample_file"><![CDATA[#slurp
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36 #if $sec_default.rename_samples.samples_src == 'entry'
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37 $sec_default.rename_samples.sample_lines.__str__.strip()#slurp
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38 #end if]]></configfile>
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39 </configfiles>
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40
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41 <inputs>
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42 <expand macro="macro_input" />
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43 <section name="sec_default" expanded="true" title="Default Options">
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44 <param name="header" type="data" format="vcf" label="Header" optional="True" help="New header" />
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45 <conditional name="rename_samples">
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46 <param name="samples_src" type="select" label="New Sample names">
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47 <help><![CDATA[
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48 New sample names, one name per line, in the same order as they appear in the VCF file.
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49 Alternatively, only samples which need to be renamed can be listed as
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50 "old_name new_name" pairs separated by whitespaces, each on separate line.
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51 ]]></help>
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52 <option value="none">Do not change</option>
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53 <option value="history">From your history</option>
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54 <option value="entry">From text input</option>
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55 </param>
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56 <when value="none"/>
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57 <when value="history">
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58 <param name="sample_file" type="data" format="tabular" label="Samples file"/>
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59 </when>
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60 <when value="entry">
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61 <param name="sample_lines" type="text" area="True" label="Samples text entry" >
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62 <validator type="regex" message="Either one name per line, or old new sample names per line">^((\S+(\n\S+))|(\S+[ \t]\S+(\n\S+[ \t]\S+)*))$</validator>
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63 <sanitizer sanitize="False"/>
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64 </param>
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65 </when>
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66 </conditional>
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67 </section>
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68 <expand macro="macro_select_output_type" />
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69 </inputs>
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70 <outputs>
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71 <expand macro="macro_vcf_output"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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76 <param name="header" ftype="vcf" value="reheader.hdr" />
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77 <param name="output_type" value="v" />
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78 <output name="output_file">
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79 <assert_contents>
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80 <has_text text="##fileformat=VCFv4.2" />
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81 <has_text text="AAA0001" />
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82 <not_has_text text="XY00001" />
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83 </assert_contents>
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84 </output>
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85 </test>
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86 <test>
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87 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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88 <param name="samples_src" value="history" />
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89 <param name="sample_file" ftype="tabular" value="reheader.samples" />
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90 <param name="output_type" value="v" />
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91 <output name="output_file">
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92 <assert_contents>
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93 <not_has_text text="XY00001" />
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94 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98 <test>
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99 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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100 <param name="samples_src" value="history" />
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101 <param name="sample_file" ftype="tabular" value="reheader.samples2" />
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102 <param name="output_type" value="v" />
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103 <output name="output_file">
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104 <assert_contents>
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105 <not_has_text text="XY00001" />
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106 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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107 </assert_contents>
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108 </output>
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109 </test>
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110 <test>
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111 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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112 <param name="samples_src" value="entry" />
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113 <param name="sample_lines" value="AAA\nBBB\n" />
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114 <param name="output_type" value="v" />
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115 <output name="output_file">
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116 <assert_contents>
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117 <not_has_text text="XY00001" />
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118 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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119 </assert_contents>
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120 </output>
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121 </test>
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122 <test>
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123 <param name="input_file" ftype="vcf" value="reheader.vcf" />
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124 <param name="samples_src" value="entry" />
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125 <param name="sample_lines" value="XY00002 BBB\nXY00001 AAA" />
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126 <param name="output_type" value="v" />
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127 <output name="output_file">
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128 <assert_contents>
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129 <not_has_text text="XY00001" />
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130 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
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131 </assert_contents>
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132 </output>
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 =====================================
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137 bcftools @EXECUTABLE@
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138 =====================================
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139
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140 Modify header of VCF/BCF files, change sample names.
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141
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142 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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143
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144 @BCFTOOLS_WIKI@
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145 ]]>
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146 </help>
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147 <expand macro="citations" />
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148 </tool>