Mercurial > repos > iuc > bcftools_reheader

comparison bcftools_reheader.xml @ 25:da7365baa407 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:58:37 +0000
parents d0933084cba7
children
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equal deleted inserted replaced
24:083211a34315 25:da7365baa407
7 </macros> 7 </macros>
8 <expand macro="bio_tools" /> 8 <expand macro="bio_tools" />
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 @PREPARE_ENV@
13 @PREPARE_INPUT_FILE@ 12 @PREPARE_INPUT_FILE@
14 bcftools @EXECUTABLE@ 13 bcftools @EXECUTABLE@
15 14
16 #set $section = $sec_default 15 #set $section = $sec_default
17 16
72 <expand macro="macro_vcf_output"/> 71 <expand macro="macro_vcf_output"/>
73 </outputs> 72 </outputs>
74 <tests> 73 <tests>
75 <test> 74 <test>
76 <param name="input_file" ftype="vcf" value="reheader.vcf" /> 75 <param name="input_file" ftype="vcf" value="reheader.vcf" />
77 <param name="header" ftype="vcf" value="reheader.hdr" /> 76 <section name="sec_default">
77 <param name="header" ftype="vcf" value="reheader.hdr" />
78 </section>
78 <param name="output_type" value="v" /> 79 <param name="output_type" value="v" />
79 <output name="output_file"> 80 <output name="output_file">
80 <assert_contents> 81 <assert_contents>
81 <has_text text="##fileformat=VCFv4.2" /> 82 <has_text text="##fileformat=VCFv4.2" />
82 <has_text text="AAA0001" /> 83 <has_text text="AAA0001" />
84 </assert_contents> 85 </assert_contents>
85 </output> 86 </output>
86 </test> 87 </test>
87 <test> 88 <test>
88 <param name="input_file" ftype="vcf" value="reheader.vcf" /> 89 <param name="input_file" ftype="vcf" value="reheader.vcf" />
89 <param name="samples_src" value="history" /> 90 <section name="sec_default">
90 <param name="sample_file" ftype="tabular" value="reheader.samples" /> 91 <conditional name="rename_samples">
92 <param name="samples_src" value="history" />
93 <param name="sample_file" ftype="tabular" value="reheader.samples" />
94 </conditional>
95 </section>
91 <param name="output_type" value="v" /> 96 <param name="output_type" value="v" />
92 <output name="output_file"> 97 <output name="output_file">
93 <assert_contents> 98 <assert_contents>
94 <not_has_text text="XY00001" /> 99 <not_has_text text="XY00001" />
95 <has_text_matching expression="FORMAT\tAAA\tBBB"/> 100 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
96 </assert_contents> 101 </assert_contents>
97 </output> 102 </output>
98 </test> 103 </test>
99 <test> 104 <test>
100 <param name="input_file" ftype="vcf" value="reheader.vcf" /> 105 <param name="input_file" ftype="vcf" value="reheader.vcf" />
101 <param name="samples_src" value="history" /> 106 <section name="sec_default">
102 <param name="sample_file" ftype="tabular" value="reheader.samples2" /> 107 <conditional name="rename_samples">
108 <param name="samples_src" value="history" />
109 <param name="sample_file" ftype="tabular" value="reheader.samples2" />
110 </conditional>
111 </section>
103 <param name="output_type" value="v" /> 112 <param name="output_type" value="v" />
104 <output name="output_file"> 113 <output name="output_file">
105 <assert_contents> 114 <assert_contents>
106 <not_has_text text="XY00001" /> 115 <not_has_text text="XY00001" />
107 <has_text_matching expression="FORMAT\tAAA\tBBB"/> 116 <has_text_matching expression="FORMAT\tAAA\tBBB"/>
142 151
143 Modify header of VCF/BCF files, change sample names. 152 Modify header of VCF/BCF files, change sample names.
144 153
145 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 154 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
146 155
147 @BCFTOOLS_WIKI@ 156 @BCFTOOLS_HOWTOS@
148 ]]> 157 ]]>
149 </help> 158 </help>
150 <expand macro="citations" /> 159 <expand macro="citations" />
151 </tool> 160 </tool>