Mercurial > repos > iuc > bcftools_isec

annotate bcftools_isec.xml @ 17:5f27e814a119 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:52:08 +0000
parents 81e4014fa809
children d7d1663559e9
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Create intersections, unions and complements of VCF files</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">isec</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 @PREPARE_ENV@
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13 @PREPARE_INPUT_FILES@
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14 #set $section = $sec_restrict
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15 @PREPARE_TARGETS_FILE@
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16 @PREPARE_REGIONS_FILE@
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18 bcftools @EXECUTABLE@
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20 ## Default section
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21 #set $section = $sec_default
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22 ${section.complement}
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23 #if $section.nfiles:
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24 --nfiles "${section.nfiles}"
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25 #end if
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27 #set $section = $sec_restrict
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28 @REGIONS@
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29 @TARGETS@
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30 @COLLAPSE@
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31 @APPLY_FILTERS@
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32 @INCLUDE@
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33 @EXCLUDE@
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35 @OUTPUT_TYPE@
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36 @THREADS@
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37
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38 ## Primary Input/Outputs
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39 @INPUT_FILES@
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40 > '$output_file'
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41
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42 ]]>
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43 </command>
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44 <inputs>
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45 <expand macro="macro_inputs" />
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46 <section name="sec_restrict" expanded="false" title="Restrict to">
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47 <expand macro="macro_collapse" />
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48 <expand macro="macro_include" />
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49 <expand macro="macro_exclude" />
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50 <expand macro="macro_apply_filters" />
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51 <expand macro="macro_restrict" />
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52 <expand macro="macro_restrict" type="target" label_type="Target" />
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53 </section>
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54 <section name="sec_default" expanded="true" title="Isec Options">
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55 <param name="nfiles" type="text" label="Nfiles" optional="True"
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56 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files" >
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57 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
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58 </param>
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59 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement"
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60 help="Output positions present only in the first file but missing in the others" />
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61 <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files"
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62 help="(-p)" />-->
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63 <!-- <param name="write" type="text" label="Files to write" optional="True"
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64 help="(-write) The output files to write " >
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65 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
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66 </param>-->
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67 </section>
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68 <expand macro="macro_select_output_type" />
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69 </inputs>
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70 <outputs>
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71 <expand macro="macro_vcf_output"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
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76 <param name="nfiles" value="=2" />
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77 <param name="output_type" value="v" />
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78 <output name="output_file">
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79 <assert_contents>
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80 <has_text text="3157410" />
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81 <has_text text="3162006" />
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82 <not_has_text text="3062915" />
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83 </assert_contents>
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84 </output>
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85 </test>
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86 <!-- Test region overlap option -->
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87 <test>
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88 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
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89 <param name="nfiles" value="=2" />
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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 <param name="regions_overlap" value="1"/>
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93 </section>
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94 <output name="output_file">
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95 <assert_contents>
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96 <has_text text="3157410" />
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97 <has_text text="3162006" />
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98 <not_has_text text="3062915" />
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99 </assert_contents>
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100 </output>
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101 <assert_command>
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102 <has_text text="--regions-overlap" />
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103 </assert_command>
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104 </test>
0
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105 </tests>
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106 <help><![CDATA[
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107 =====================================
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108 bcftools @EXECUTABLE@
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109 =====================================
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110
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111 Create intersections, unions and complements of VCF files.
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112
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113 @COLLAPSE_HELP@
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114 @REGIONS_HELP@
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115 @TARGETS_HELP@
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116 @EXPRESSIONS_HELP@
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117
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118 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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119
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120 @BCFTOOLS_WIKI@
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121 ]]>
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122 </help>
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123 <expand macro="citations" />
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124 </tool>