Mercurial > repos > iuc > bcftools_plugin_dosage

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
author iuc
date Sun, 18 Aug 2024 10:20:20 +0000
parents 2514e684f8a3
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1 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>plugin genotype dosage</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">dosage</token>
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5 <token name="@PLUGIN_ID@">dosage</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools" />
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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 ## Primary Input/Outputs
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28 @INPUT_FILE@
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30 ## Plugin section
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31 #set $section = $sec_plugin
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32 #if $section.tags:
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33 -- --tags "${section.tags}"
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34 #end if
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35 > '$output_file'
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37 ]]>
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38 </command>
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39 <inputs>
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40 <expand macro="macro_input" />
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41 <section name="sec_restrict" expanded="false" title="Restrict to">
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42 <expand macro="macro_restrict" />
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43 <expand macro="macro_restrict" type="target" label_type="Target" />
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44 <expand macro="macro_include" />
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45 <expand macro="macro_exclude" />
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46 </section>
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47 <section name="sec_plugin" expanded="true" title="Plugin Options">
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48 <param name="tags" type="text" value="" optional="true" label="VCF tag to determine the dosage from [PL,GL,GT]">
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49 <validator type="regex" message="Tags separated by commas">^(PL|GL|GT)(,(PL|GL|GT))*$</validator>
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50 </param>
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51 </section>
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52 </inputs>
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53 <outputs>
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54 <data name="output_file" format="tabular"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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59 <output name="output_file">
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60 <assert_contents>
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61 <has_text_matching expression="#\[1]CHROM\t\[2]POS\t\[3]REF\t\[4]ALT\t\[5]A\t\[6]B"/>
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62 <has_text_matching expression="1\t3157410\tGA\tG\t2.0\t2.0"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 =====================================
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69 bcftools @EXECUTABLE@ plugin
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70 =====================================
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71
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72 @REGIONS_HELP@
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73 @TARGETS_HELP@
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74 @EXPRESSIONS_HELP@
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75
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>