Mercurial > repos > iuc > bcftools_gtcheck

comparison bcftools_gtcheck.xml @ 25:d6f8a234358c 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 07:45:56 +0000
parents b3732c5629a4
children
comparison
equal deleted inserted replaced
24:b3732c5629a4 25:d6f8a234358c
6 </macros> 6 </macros>
7 <expand macro="bio_tools" /> 7 <expand macro="bio_tools" />
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@ 11 @PREPARE_INPUT_FILE@
13 #set $section = $sec_restrict 12 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 13 @PREPARE_TARGETS_FILE@
15 @PREPARE_REGIONS_FILE@ 14 @PREPARE_REGIONS_FILE@
16 #set $section = $sec_default 15 #set $section = $sec_default
71 ]]> 70 ]]>
72 </command> 71 </command>
73 <inputs> 72 <inputs>
74 <expand macro="macro_input" /> 73 <expand macro="macro_input" />
75 <section name="sec_restrict" expanded="false" title="Restrict to"> 74 <section name="sec_restrict" expanded="false" title="Restrict to">
76 <expand macro="macro_restrict" /> 75 <expand macro="macro_region_restrict" />
77 <expand macro="macro_restrict" type="target" label_type="Target" /> 76 <expand macro="macro_target_restrict" />
78 </section> 77 </section>
79 <section name="sec_default" expanded="true" title="Default Options"> 78 <section name="sec_default" expanded="true" title="Default Options">
80 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" 79 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
81 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/> 80 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
82 <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" /> 81 <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
92 <tests> 91 <tests>
93 <test> 92 <test>
94 <param name="input_file" ftype="vcf" value="view.vcf" /> 93 <param name="input_file" ftype="vcf" value="view.vcf" />
95 <output name="output_file"> 94 <output name="output_file">
96 <assert_contents> 95 <assert_contents>
97 <has_text_matching expression="DC\tNA00002\tNA00001\t6"/> 96 <has_text_matching expression="DCv2\tNA00002\tNA00001\t6"/>
98 </assert_contents> 97 </assert_contents>
99 </output> 98 </output>
100 </test> 99 </test>
101 </tests> 100 </tests>
102 <help><![CDATA[ 101 <help><![CDATA[
109 @REGIONS_HELP@ 108 @REGIONS_HELP@
110 @TARGETS_HELP@ 109 @TARGETS_HELP@
111 110
112 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 111 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
113 112
114 @BCFTOOLS_WIKI@ 113 @BCFTOOLS_HOWTOS@
115 114
116 ]]> 115 ]]>
117 </help> 116 </help>
118 <expand macro="citations" /> 117 <expand macro="citations" />
119 </tool> 118 </tool>