Mercurial > repos > iuc > bcftools_plugin_setgt

comparison bcftools_plugin_setgt.xml @ 25:a5669238dbcc 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 07:44:36 +0000
parents 3e44f68c5f79
children
comparison
equal deleted inserted replaced
24:3e44f68c5f79 25:a5669238dbcc
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 #set $section = $sec_restrict 13 #set $section = $sec_restrict
15 @PREPARE_TARGETS_FILE@ 14 @PREPARE_TARGETS_FILE@
16 @PREPARE_REGIONS_FILE@ 15 @PREPARE_REGIONS_FILE@
17 bcftools plugin @EXECUTABLE@ 16 bcftools plugin @EXECUTABLE@
40 ]]> 39 ]]>
41 </command> 40 </command>
42 <inputs> 41 <inputs>
43 <expand macro="macro_input" /> 42 <expand macro="macro_input" />
44 <section name="sec_restrict" title="Restrict to"> 43 <section name="sec_restrict" title="Restrict to">
45 <expand macro="macro_restrict" /> 44 <expand macro="macro_region_restrict" />
46 <expand macro="macro_restrict" type="target" label_type="Target" /> 45 <expand macro="macro_target_restrict" />
47 <expand macro="macro_include" /> 46 <expand macro="macro_include" />
48 <expand macro="macro_exclude" /> 47 <expand macro="macro_exclude" />
49 </section> 48 </section>
50 <section name="sec_plugin" expanded="true" title="Plugin Options"> 49 <section name="sec_plugin" expanded="true" title="Plugin Options">
51 <param name="target_gt" type="select" label="Target genotypes to change"> 50 <param name="target_gt" type="select" label="Target genotypes to change">
58 </param> 57 </param>
59 <param name="new_gt" type="select" label="New genotypes to set"> 58 <param name="new_gt" type="select" label="New genotypes to set">
60 <option value=".">. missing (. or ./., keeps ploidy)</option> 59 <option value=".">. missing (. or ./., keeps ploidy)</option>
61 <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option> 60 <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option>
62 <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option> 61 <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option>
62 <option value="c:./.">c:./. missing genotype with arbitrary ploidy</option>
63 <option value="M">M major allele</option> 63 <option value="M">M major allele</option>
64 <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option> 64 <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option>
65 <option value="p">p phased genotype</option> 65 <option value="p">p phased genotype</option>
66 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option> 66 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option>
67 </param> 67 </param>
72 <expand macro="macro_vcf_output" /> 72 <expand macro="macro_vcf_output" />
73 </outputs> 73 </outputs>
74 <tests> 74 <tests>
75 <test> 75 <test>
76 <param name="input_file" ftype="vcf" value="plugin1.vcf" /> 76 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
77 <param name="target_gt" value="." /> 77 <section name="sec_plugin">
78 <param name="new_gt" value="0" /> 78 <param name="target_gt" value="." />
79 <param name="new_gt" value="0" />
80 </section>
79 <param name="output_type" value="v" /> 81 <param name="output_type" value="v" />
80 <output name="output_file"> 82 <output name="output_file">
81 <assert_contents> 83 <assert_contents>
82 <has_text text="0/0:245" /> 84 <has_text text="0/0:245" />
83 </assert_contents> 85 </assert_contents>
98 <has_text text="DP4=1,2,3,4;INDEL;STR=test" /> 100 <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
99 <has_n_lines n="38"/> 101 <has_n_lines n="38"/>
100 </assert_contents> 102 </assert_contents>
101 </output> 103 </output>
102 </test> 104 </test>
105 <test>
106 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
107 <section name="sec_plugin">
108 <param name="target_gt" value="." />
109 <param name="new_gt" value="c:./." />
110 </section>
111 <param name="output_type" value="v" />
112 <output name="output_file">
113 <assert_contents>
114 <has_text text="GT" />
115 <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
116 </assert_contents>
117 </output>
118 </test>
103 </tests> 119 </tests>
104 <help><![CDATA[ 120 <help><![CDATA[
105 ===================================== 121 =====================================
106 bcftools @EXECUTABLE@ plugin 122 bcftools @EXECUTABLE@ plugin
107 ===================================== 123 =====================================