Mercurial > repos > iuc > bcftools_isec

annotate bcftools_isec.xml @ 25:df29f44b1bc0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 09:42:36 +0000
parents 8711939e09b1
children a2e8d800df1f
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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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a0e25d370c6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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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_ENV@
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12 @PREPARE_INPUT_FILES@
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13 #set $section = $sec_restrict
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14 @PREPARE_TARGETS_FILE@
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15 @PREPARE_REGIONS_FILE@
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17 bcftools @EXECUTABLE@
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19 ## Default section
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20 #set $section = $sec_default
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21 ${section.complement}
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22 #if $section.nfiles:
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23 --nfiles "${section.nfiles}"
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24 #end if
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26 #set $section = $sec_restrict
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27 @REGIONS@
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28 @TARGETS@
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29 @COLLAPSE@
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30 @APPLY_FILTERS@
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31 @INCLUDE@
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32 @EXCLUDE@
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34 @OUTPUT_TYPE@
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35 @THREADS@
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36
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37 ## Primary Input/Outputs
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38 @INPUT_FILES@
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39 > '$output_file'
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40
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41 ]]>
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42 </command>
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43 <inputs>
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44 <expand macro="macro_inputs" />
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45 <section name="sec_restrict" expanded="false" title="Restrict to">
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46 <expand macro="macro_collapse" />
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47 <expand macro="macro_include" />
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48 <expand macro="macro_exclude" />
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49 <expand macro="macro_apply_filters" />
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50 <expand macro="macro_restrict" />
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51 <expand macro="macro_restrict" type="target" label_type="Target" />
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52 </section>
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53 <section name="sec_default" expanded="true" title="Isec Options">
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54 <param argument="--nfiles" type="text" label="Nfiles"
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55 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files">
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56 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
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57 </param>
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58 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement"
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59 help="Output positions present only in the first file but missing in the others" />
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60 <!-- <param name="prefix" type="boolean" truevalue="\-\-prefix subset" falsevalue="" checked="false" label="subset each of the input files"
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61 help="(-p)" />-->
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62 <!-- <param name="write" type="text" label="Files to write" optional="True"
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63 help="(-write) The output files to write " >
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64 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
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65 </param>-->
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66 </section>
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67 <expand macro="macro_select_output_type" />
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68 </inputs>
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69 <outputs>
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70 <expand macro="macro_vcf_output"/>
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
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75 <param name="nfiles" value="=2" />
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76 <param name="output_type" value="v" />
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77 <output name="output_file">
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78 <assert_contents>
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79 <has_text text="3157410" />
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80 <has_text text="3162006" />
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81 <not_has_text text="3062915" />
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82 </assert_contents>
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83 </output>
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84 </test>
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85 <!-- Test region overlap option -->
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86 <test>
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87 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
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88 <param name="nfiles" value="=2" />
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89 <param name="output_type" value="v" />
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90 <section name="sec_restrict">
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91 <param name="regions_overlap" value="1"/>
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92 </section>
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93 <output name="output_file">
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94 <assert_contents>
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95 <has_text text="3157410" />
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96 <has_text text="3162006" />
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97 <not_has_text text="3062915" />
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98 </assert_contents>
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99 </output>
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100 <assert_command>
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101 <has_text text="--regions-overlap" />
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102 </assert_command>
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103 </test>
0
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104 </tests>
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105 <help><![CDATA[
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106 =====================================
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107 bcftools @EXECUTABLE@
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108 =====================================
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109
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110 Create intersections, unions and complements of VCF files.
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111
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112 @COLLAPSE_HELP@
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113 @REGIONS_HELP@
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114 @TARGETS_HELP@
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115 @EXPRESSIONS_HELP@
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116
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117 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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118
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119 @BCFTOOLS_WIKI@
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120 ]]>
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121 </help>
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122 <expand macro="citations" />
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123 </tool>