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comparison bcftools_isec.xml @ 26:a2e8d800df1f 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 07:46:38 +0000
parents df29f44b1bc0
children
comparison
equal deleted inserted replaced
25:df29f44b1bc0 26:a2e8d800df1f
2 <description>Create intersections, unions and complements of VCF files</description> 2 <description>Create intersections, unions and complements of VCF files</description>
3 <macros> 3 <macros>
4 <token name="@EXECUTABLE@">isec</token> 4 <token name="@EXECUTABLE@">isec</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
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_FILES@ 11 @PREPARE_INPUT_FILES@
13 #set $section = $sec_restrict 12 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 13 @PREPARE_TARGETS_FILE@
15 @PREPARE_REGIONS_FILE@ 14 @PREPARE_REGIONS_FILE@
16 15
39 > '$output_file' 38 > '$output_file'
40 39
41 ]]> 40 ]]>
42 </command> 41 </command>
43 <inputs> 42 <inputs>
44 <expand macro="macro_inputs" /> 43 <expand macro="macro_inputs"/>
45 <section name="sec_restrict" expanded="false" title="Restrict to"> 44 <section name="sec_restrict" expanded="false" title="Restrict to">
46 <expand macro="macro_collapse" /> 45 <expand macro="macro_collapse"/>
47 <expand macro="macro_include" /> 46 <expand macro="macro_include"/>
48 <expand macro="macro_exclude" /> 47 <expand macro="macro_exclude"/>
49 <expand macro="macro_apply_filters" /> 48 <expand macro="macro_apply_filters"/>
50 <expand macro="macro_restrict" /> 49 <expand macro="macro_region_restrict"/>
51 <expand macro="macro_restrict" type="target" label_type="Target" /> 50 <expand macro="macro_target_restrict"/>
52 </section> 51 </section>
53 <section name="sec_default" expanded="true" title="Isec Options"> 52 <section name="sec_default" expanded="true" title="Isec Options">
54 <param argument="--nfiles" type="text" label="Nfiles" 53 <param argument="--nfiles" type="text" label="Nfiles" help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files">
55 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files">
56 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator> 54 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
57 </param> 55 </param>
58 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" 56 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" help="Output positions present only in the first file but missing in the others"/>
59 help="Output positions present only in the first file but missing in the others" />
60 <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files" 57 <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files"
61 help="(-p)" />--> 58 help="(-p)" />-->
62 <!-- <param name="write" type="text" label="Files to write" optional="True" 59 <!-- <param name="write" type="text" label="Files to write" optional="True"
63 help="(-write) The output files to write " > 60 help="(-write) The output files to write " >
64 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator> 61 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
65 </param>--> 62 </param>-->
66 </section> 63 </section>
67 <expand macro="macro_select_output_type" /> 64 <expand macro="macro_select_output_type"/>
68 </inputs> 65 </inputs>
69 <outputs> 66 <outputs>
70 <expand macro="macro_vcf_output"/> 67 <expand macro="macro_vcf_output"/>
71 </outputs> 68 </outputs>
72 <tests> 69 <tests>
73 <test> 70 <test>
74 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" /> 71 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
75 <param name="nfiles" value="=2" /> 72 <section name="sec_default">
76 <param name="output_type" value="v" /> 73 <param name="nfiles" value="=2"/>
74 </section>
75 <param name="output_type" value="v"/>
77 <output name="output_file"> 76 <output name="output_file">
78 <assert_contents> 77 <assert_contents>
79 <has_text text="3157410" /> 78 <has_text text="3157410"/>
80 <has_text text="3162006" /> 79 <has_text text="3162006"/>
81 <not_has_text text="3062915" /> 80 <not_has_text text="3062915"/>
82 </assert_contents> 81 </assert_contents>
83 </output> 82 </output>
84 </test> 83 </test>
85 <!-- Test region overlap option --> 84 <!-- Test region overlap option -->
86 <test> 85 <test>
87 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" /> 86 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
88 <param name="nfiles" value="=2" /> 87 <section name="sec_default">
89 <param name="output_type" value="v" /> 88 <param name="nfiles" value="=2"/>
89 </section>
90 <param name="output_type" value="v"/>
90 <section name="sec_restrict"> 91 <section name="sec_restrict">
91 <param name="regions_overlap" value="1"/> 92 <conditional name="regions">
93 <param name="regions_src" value="regions" />
94 <repeat name="region_specs">
95 <param name="chrom" value="1" />
96 </repeat>
97 </conditional>
92 </section> 98 </section>
93 <output name="output_file"> 99 <output name="output_file">
94 <assert_contents> 100 <assert_contents>
95 <has_text text="3157410" /> 101 <has_text text="3157410"/>
96 <has_text text="3162006" /> 102 <has_text text="3162006"/>
97 <not_has_text text="3062915" /> 103 <not_has_text text="3062915"/>
98 </assert_contents> 104 </assert_contents>
99 </output> 105 </output>
100 <assert_command> 106 <assert_command>
101 <has_text text="--regions-overlap" /> 107 <has_text text="--regions-overlap"/>
102 </assert_command> 108 </assert_command>
103 </test> 109 </test>
104 </tests> 110 </tests>
105 <help><![CDATA[ 111 <help><![CDATA[
106 ===================================== 112 =====================================
114 @TARGETS_HELP@ 120 @TARGETS_HELP@
115 @EXPRESSIONS_HELP@ 121 @EXPRESSIONS_HELP@
116 122
117 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 123 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
118 124
119 @BCFTOOLS_WIKI@ 125 @BCFTOOLS_HOWTOS@
120 ]]> 126 ]]>
121 </help> 127 </help>
122 <expand macro="citations" /> 128 <expand macro="citations"/>
123 </tool> 129 </tool>