Mercurial > repos > iuc > bcftools_plugin_tag2tag

annotate bcftools_plugin_tag2tag.xml @ 14:8aa9d9b14bcd 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 833751f38971a1957a9e16d09acf62cdf6048ad9"
author iuc
date Tue, 19 Oct 2021 15:34:03 +0000
parents f272b8ba0983
children f35cc95efb32
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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="@TOOL_VERSION@+galaxy1">
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3 <description>plugin Convert between similar tags, such as GL and GP</description>
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4 <expand macro="bio_tools" />
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5 <macros>
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6 <token name="@EXECUTABLE@">tag2tag</token>
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7 <token name="@PLUGIN_ID@">tag2tag</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements" />
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11 <expand macro="version_command" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 @PREPARE_ENV@
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14 @PREPARE_INPUT_FILE@
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15 #set $section = $sec_restrict
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16 @PREPARE_TARGETS_FILE@
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17 @PREPARE_REGIONS_FILE@
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19 bcftools plugin @EXECUTABLE@
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21 ## VCF input section
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22 #set $section = $sec_restrict
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23 @INCLUDE@
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24 @EXCLUDE@
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25 @REGIONS@
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26 @TARGETS@
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28 @OUTPUT_TYPE@
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29 @THREADS@
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31 ## Primary Input/Outputs
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32 @INPUT_FILE@
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34 ## Plugin section
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35 #set $section = $sec_plugin
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36 --
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37 ${section.conversion}
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38 ${section.replace}
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39 #if $section.conversion == '--gp-to-gt' and float($section.threshold) is not None:
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40 --threshold ${section.threshold}
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41 #end if
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42 > '$output_file'
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43 ]]>
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44 </command>
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45 <inputs>
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46 <expand macro="macro_input" />
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47 <section name="sec_restrict" expanded="false" title="Restrict to">
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48 <expand macro="macro_restrict" />
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49 <expand macro="macro_restrict" type="target" label_type="Target" />
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50 <expand macro="macro_include" />
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51 <expand macro="macro_exclude" />
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52 </section>
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53 <section name="sec_plugin" expanded="true" title="Plugin Options">
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54 <param name="conversion" type="select" label="Tag conversion">
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55 <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option>
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56 <option value="--gp-to-gt" selected="true">convert FORMAT/GP to FORMAT/GT (by taking argmax of GP)</option>
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57 <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option>
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58 <option value="--pl-to-gl">convert FORMAT/PL to FORMAT/GL</option>
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59 </param>
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60 <param argument="--replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="Drop the source tag" />
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61 <param argument="--threshold" type="float" value=".1" min="0." max="1.0" optional="true" label="Threshold for GP to GT hard-call" />
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62 </section>
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63 <expand macro="macro_select_output_type" />
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64 </inputs>
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65 <outputs>
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66 <expand macro="macro_vcf_output" />
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="input_file" ftype="vcf" value="view.GL.vcf" />
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71 <param name="replace" value="True" />
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72 <param name="conversion" value="--gl-to-pl" />
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73 <param name="output_type" value="v" />
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74 <output name="output_file">
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75 <assert_contents>
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76 <has_text text="ID=PL,"/>
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 =====================================
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83 bcftools @EXECUTABLE@ plugin
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84 =====================================
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85
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86 @REGIONS_HELP@
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87 @TARGETS_HELP@
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88 @EXPRESSIONS_HELP@
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89
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90 ]]></help>
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91 <expand macro="citations" />
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92 </tool>