Mercurial > repos > iuc > bcftools_plugin_tag2tag

annotate bcftools_plugin_tag2tag.xml @ 11:aa998b9898b1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
author iuc
date Wed, 25 Dec 2019 12:27:13 -0500
parents 2f8261ee0ea9
children f272b8ba0983
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1 <?xml version='1.0' encoding='utf-8'?>
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aa998b9898b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
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3 <description>plugin Convert between similar tags, such as GL and GP</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">tag2tag</token>
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6 <token name="@PLUGIN_ID@">tag2tag</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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29
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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 --
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36 ${section.conversion}
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37 ${section.replace}
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38 #if $section.conversion == '--gp-to-gt' and float($section.threshold) is not None:
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39 --threshold ${section.threshold}
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40 #end if
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41 > '$output_file'
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42 ]]>
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43 </command>
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44 <inputs>
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45 <expand macro="macro_input" />
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46 <section name="sec_restrict" expanded="false" title="Restrict to">
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47 <expand macro="macro_restrict" />
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48 <expand macro="macro_restrict" type="target" label_type="Target" />
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49 <expand macro="macro_include" />
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50 <expand macro="macro_exclude" />
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51 </section>
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52 <section name="sec_plugin" expanded="true" title="Plugin Options">
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53 <param name="conversion" type="select" label="Tag conversion">
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54 <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option>
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55 <option value="--gp-to-gt" selected="true">convert FORMAT/GP to FORMAT/GT (by taking argmax of GP)</option>
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56 <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option>
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57 <option value="--pl-to-gl">convert FORMAT/PL to FORMAT/GL</option>
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58 </param>
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59 <param name="replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="drop the source tag" help="(\-\-replace)" />
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60 <param name="" type="float" value=".1" min="0." max="1.0" optional="true" label="threshold for GP to GT hard-call" help="(\-\-threshold float)" />
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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="view.GL.vcf" />
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70 <param name="replace" value="True" />
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71 <param name="conversion" value="--gl-to-pl" />
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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="ID=PL,"/>
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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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86 @TARGETS_HELP@
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87 @EXPRESSIONS_HELP@
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88
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89 ]]></help>
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90 <expand macro="citations" />
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91 </tool>