Mercurial > repos > iuc > bcftools_plugin_fixploidy

annotate bcftools_plugin_fixploidy.xml @ 4:b7dc6f8084ce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:01:42 -0500
parents 7d6599c7e2fb
children aec8cc772e0c
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7d6599c7e2fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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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@">
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3 <description>plugin Fix ploidy</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">fixploidy</token>
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6 <token name="@PLUGIN_ID@">fixploidy</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 --
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35 @PLOIDY_FILE@
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36 #if $section.sex:
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37 --sex "${section.sex}"
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38 #end if
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39 ## Only default tag GT is currently accepted
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40 --tags "$section.tags"
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41 > "$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_regions" />
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48 <expand macro="macro_targets" />
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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 <expand macro="macro_ploidy_file" />
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54 <param name="sex" type="data" format="tabular" label="Sample Sex file" optional="true"/>
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55 <param name="tags" type="hidden" value="GT" label="tags"/>
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56 </section>
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57 <expand macro="macro_select_output_type" />
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58 </inputs>
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59 <outputs>
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60 <expand macro="macro_vcf_output" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input_file" ftype="vcf" value="fixploidy.vcf" />
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65 <param name="sex" ftype="tabular" value="fixploidy.samples" />
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66 <param name="ploidy_file" ftype="tabular" value="fixploidy.ploidy" />
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67 <param name="output_type" value="v" />
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68 <output name="output_file">
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69 <assert_contents>
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70 <has_text_matching expression="3000004\txx\tC\tCTTTT\t11\tq11\tFLAG;IINT=11;IFLT=1.1;ISTR=xxx\tGT:FINT:FFLT:FSTR\t0/0/0/0/0/0:11:1.1:x\t0/0/0/0/0/0/0:11:1.1:xxx\t0|0|0|0|0|0|0|0:11:1.1:xxx" />
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71 </assert_contents>
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72 </output>
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73 </test>
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74 </tests>
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75 <help><![CDATA[
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76 =====================================
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77 bcftools @EXECUTABLE@ plugin
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78 =====================================
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79
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80 @REGIONS_HELP@
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81 @TARGETS_HELP@
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82 @EXPRESSIONS_HELP@
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83
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84 ]]></help>
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85 <expand macro="citations" />
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86 </tool>