Mercurial > repos > iuc > bcftools_plugin_missing2ref

annotate bcftools_plugin_missing2ref.xml @ 5:17e1e452297b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:46:23 -0400
parents 64b2f65980ea
children 31c096c6b156
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@">
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3 <description>plugin Set missing genotypes</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">missing2ref</token>
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6 <token name="@PLUGIN_ID@">missing2ref</token>
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7 <import>macros.xml</import>
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8 </macros>
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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_FILE@
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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 plugin @EXECUTABLE@
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20 ## VCF input section
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21 #set $section = $sec_restrict
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22 @INCLUDE@
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23 @EXCLUDE@
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24 @REGIONS@
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25 @TARGETS@
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27 @OUTPUT_TYPE@
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28 @THREADS@
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30 ## Primary Input/Outputs
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31 @INPUT_FILE@
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32
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33 ## Plugin section
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34 #set $section = $sec_plugin
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35 #if $section.phased or $section.major:
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36 --
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37 ${section.phased}
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38 ${section.major}
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39 #end if
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40 > '$output_file'
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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_input" />
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45 <section name="sec_restrict" expanded="false" title="Restrict to">
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46 <expand macro="macro_regions" />
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47 <expand macro="macro_targets" />
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48 <expand macro="macro_include" />
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49 <expand macro="macro_exclude" />
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50 </section>
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51 <section name="sec_plugin" expanded="true" title="Plugin Options">
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52 <param name="phased" type="boolean" truevalue="--phased" falsevalue="" checked="false" label="Phased" help="Set to 0|0" />
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53 <param name="major" type="boolean" truevalue="--major" falsevalue="" checked="false" label="Major" help="Set to major allele" />
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54 </section>
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55 <expand macro="macro_select_output_type" />
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56 </inputs>
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57 <outputs>
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58 <expand macro="macro_vcf_output" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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63 <param name="output_type" value="v" />
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64 <output name="output_file">
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65 <assert_contents>
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66 <has_text text="0/0:245" />
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 =====================================
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73 bcftools @EXECUTABLE@ plugin
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74 =====================================
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75
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76 @REGIONS_HELP@
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77 @TARGETS_HELP@
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78 @EXPRESSIONS_HELP@
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79
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80 ]]></help>
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81 <expand macro="citations" />
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82 </tool>