Mercurial > repos > iuc > bcftools_isec

annotate bcftools_isec.xml @ 0:a994b57c9a7d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:03:54 -0400
parents
children 71747e4a4aa1
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0
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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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="@VERSION@.0">
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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="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
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16 bcftools @EXECUTABLE@
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17
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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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24
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25 #set $section = $sec_restrict
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26 @REGIONS@
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27 @TARGETS@
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28 @COLLAPSE@
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29 @APPLY_FILTERS@
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30 @INCLUDE@
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31 @EXCLUDE@
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32
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33 @OUTPUT_TYPE@
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34 @THREADS@
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35
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36 ## Primary Input/Outputs
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37 @INPUT_FILES@
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38 > "$output_file"
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39
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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_regions" />
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50 <expand macro="macro_targets" />
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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 name="nfiles" type="text" label="Nfiles" optional="True"
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54 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files" >
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55 <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
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56 </param>
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57 <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement"
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58 help="Output positions present only in the first file but missing in the others" />
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59 <param name="prefix" type="boolean" truevalue="--prefix subset" falsevalue="" checked="false" label="subset each of the input files"
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60 help="(-p)" />
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61 <param name="write" type="text" label="Files to write" optional="True"
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62 help="(-write) The output files to write " >
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63 <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
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64 </param>
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65 </section>
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66 <expand macro="macro_select_output_type" />
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67 </inputs>
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68 <outputs>
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69 <expand macro="macro_vcf_output"/>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
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74 <param name="nfiles" value="=2" />
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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
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85 </tests>
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86 <help><![CDATA[
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87 =====================================
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88 bcftools @EXECUTABLE@
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89 =====================================
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90
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91 Create intersections, unions and complements of VCF files.
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92
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93 @COLLAPSE_HELP@
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94 @REGIONS_HELP@
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95 @TARGETS_HELP@
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96 @EXPRESSIONS_HELP@
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98 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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100 @BCFTOOLS_WIKI@
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101 ]]>
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102 </help>
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103 <expand macro="citations" />
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104 </tool>