Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

annotate bcftools_plugin_missing2ref.xml @ 0:ff65d6e0809b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:51:04 -0400
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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@.0">
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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
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17 bcftools plugin @EXECUTABLE@
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18
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19 ## VCF input section
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20 #set $section = $sec_restrict
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21 @INCLUDE@
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22 @EXCLUDE@
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23 @REGIONS@
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24 @TARGETS@
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25
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26 @OUTPUT_TYPE@
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27 @THREADS@
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28
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29 ## Primary Input/Outputs
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30 @INPUT_FILE@
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31
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32 ## Plugin section
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33 #set $section = $sec_plugin
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34 #if $section.phased or $section.major:
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35 --
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36 ${section.phased}
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37 ${section.major}
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38 #end if
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39 > "$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_input" />
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44 <section name="sec_restrict" expanded="false" title="Restrict to">
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45 <expand macro="macro_regions" />
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46 <expand macro="macro_targets" />
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47 <expand macro="macro_include" />
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48 <expand macro="macro_exclude" />
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49 </section>
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50 <section name="sec_plugin" expanded="true" title="Plugin Options">
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51 <param name="phased" type="boolean" truevalue="--phased" falsevalue="" checked="false" label="Phased" help="Set to 0|0" />
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52 <param name="major" type="boolean" truevalue="--major" falsevalue="" checked="false" label="Major" help="Set to major allele" />
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53 </section>
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54 <expand macro="macro_select_output_type" />
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55 </inputs>
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56 <outputs>
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57 <expand macro="macro_vcf_output" />
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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62 <param name="output_type" value="v" />
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63 <output name="output_file">
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64 <assert_contents>
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65 <has_text text="0/0:245" />
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 =====================================
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72 bcftools @EXECUTABLE@ plugin
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73 =====================================
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74
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75 @REGIONS_HELP@
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76 @TARGETS_HELP@
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77 @EXPRESSIONS_HELP@
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78
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79 ]]></help>
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80 <expand macro="citations" />
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81 </tool>