Mercurial > repos > jjohnson > bcftools_plugin_setgt

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:41:21 -0400
parents 28c189385d7e
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28c189385d7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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 Sets genotypes</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">setGT</token>
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6 <token name="@PLUGIN_ID@">setgt</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 bcftools plugin @EXECUTABLE@
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17
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18 ## VCF input section
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19 #set $section = $sec_restrict
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20 @INCLUDE@
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21 @EXCLUDE@
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22 @REGIONS@
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23 @TARGETS@
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24
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25 @OUTPUT_TYPE@
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26 @THREADS@
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27
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28 ## Primary Input/Outputs
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29 @INPUT_FILE@
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30
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31 ## Plugin section
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32 #set $section = $sec_plugin
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33 --
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34 --target-gt '$section.target_gt'
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35 --new-gt '$section.new_gt'
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36 > "$output_file"
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37 ]]>
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38 </command>
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39 <inputs>
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40 <expand macro="macro_input" />
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41 <section name="sec_restrict" expanded="false" title="Restrict to">
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42 <expand macro="macro_regions" />
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43 <expand macro="macro_targets" />
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44 <expand macro="macro_include" />
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45 <expand macro="macro_exclude" />
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46 </section>
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47 <section name="sec_plugin" expanded="true" title="Plugin Options">
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48 <param name="target_gt" type="select" label="Target genotypes to change">
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49 <option value="./.">./. completely missing (. or ./., depending on ploidy)</option>
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50 <option value="./x">./x partially missing (./0 or .|1)</option>
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51 <option value=".">. partially or completely missing</option>
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52 <option value="a">a all genotypes</option>
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53 </param>
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54 <param name="new_gt" type="select" label="New genotypes to set">
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55 <option value=".">. missing (. or ./., keeps ploidy)</option>
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56 <option value="0">0 reference allele</option>
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57 <option value="M">M major allele</option>
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58 <option value="p">p phased genotype</option>
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59 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option>
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60 </param>
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61 </section>
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62 <expand macro="macro_select_output_type" />
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63 </inputs>
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64 <outputs>
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65 <expand macro="macro_vcf_output" />
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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70 <param name="target_gt" value="." />
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71 <param name="new_gt" value="0" />
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72 <param name="output_type" value="v" />
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73 <output name="output_file">
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74 <assert_contents>
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75 <has_text text="0/0:245" />
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76 </assert_contents>
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77 </output>
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78 </test>
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79 </tests>
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80 <help><![CDATA[
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81 =====================================
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82 bcftools @EXECUTABLE@ plugin
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83 =====================================
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84
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85 @REGIONS_HELP@
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jjohnson
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86 @TARGETS_HELP@
28c189385d7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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87 @EXPRESSIONS_HELP@
28c189385d7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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88
28c189385d7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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89 ]]></help>
28c189385d7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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90 <expand macro="citations" />
28c189385d7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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91 </tool>