Mercurial > repos > iuc > bcftools_isec

annotate 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
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Create intersections, unions and complements of VCF files</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">isec</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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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_INPUT_FILES@
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12 #set $section = $sec_restrict
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13 @PREPARE_TARGETS_FILE@
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14 @PREPARE_REGIONS_FILE@
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16 bcftools @EXECUTABLE@
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18 ## Default section
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19 #set $section = $sec_default
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20 ${section.complement}
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21 #if $section.nfiles:
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22 --nfiles "${section.nfiles}"
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23 #end if
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25 #set $section = $sec_restrict
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26 @REGIONS@
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27 @TARGETS@
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28 @COLLAPSE@
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29 @APPLY_FILTERS@
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30 @INCLUDE@
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31 @EXCLUDE@
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33 @OUTPUT_TYPE@
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34 @THREADS@
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36 ## Primary Input/Outputs
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37 @INPUT_FILES@
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38 > '$output_file'
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40 ]]>
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41 </command>
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42 <inputs>
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43 <expand macro="macro_inputs"/>
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44 <section name="sec_restrict" expanded="false" title="Restrict to">
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45 <expand macro="macro_collapse"/>
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46 <expand macro="macro_include"/>
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47 <expand macro="macro_exclude"/>
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48 <expand macro="macro_apply_filters"/>
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49 <expand macro="macro_region_restrict"/>
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50 <expand macro="macro_target_restrict"/>
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51 </section>
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52 <section name="sec_default" expanded="true" title="Isec Options">
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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">
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54 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
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55 </param>
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56 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" help="Output positions present only in the first file but missing in the others"/>
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57 <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files"
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58 help="(-p)" />-->
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59 <!-- <param name="write" type="text" label="Files to write" optional="True"
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60 help="(-write) The output files to write " >
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61 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
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62 </param>-->
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63 </section>
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64 <expand macro="macro_select_output_type"/>
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65 </inputs>
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66 <outputs>
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67 <expand macro="macro_vcf_output"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
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72 <section name="sec_default">
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73 <param name="nfiles" value="=2"/>
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74 </section>
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75 <param name="output_type" value="v"/>
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76 <output name="output_file">
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77 <assert_contents>
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78 <has_text text="3157410"/>
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79 <has_text text="3162006"/>
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80 <not_has_text text="3062915"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <!-- Test region overlap option -->
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85 <test>
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86 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf"/>
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87 <section name="sec_default">
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88 <param name="nfiles" value="=2"/>
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89 </section>
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90 <param name="output_type" value="v"/>
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91 <section name="sec_restrict">
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92 <conditional name="regions">
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93 <param name="regions_src" value="regions" />
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94 <repeat name="region_specs">
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95 <param name="chrom" value="1" />
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96 </repeat>
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97 </conditional>
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98 </section>
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99 <output name="output_file">
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100 <assert_contents>
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101 <has_text text="3157410"/>
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102 <has_text text="3162006"/>
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103 <not_has_text text="3062915"/>
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104 </assert_contents>
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105 </output>
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106 <assert_command>
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107 <has_text text="--regions-overlap"/>
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108 </assert_command>
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109 </test>
0
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110 </tests>
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111 <help><![CDATA[
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112 =====================================
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113 bcftools @EXECUTABLE@
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114 =====================================
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115
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116 Create intersections, unions and complements of VCF files.
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117
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118 @COLLAPSE_HELP@
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119 @REGIONS_HELP@
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120 @TARGETS_HELP@
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121 @EXPRESSIONS_HELP@
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122
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123 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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124
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125 @BCFTOOLS_HOWTOS@
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126 ]]>
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127 </help>
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128 <expand macro="citations"/>
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129 </tool>