Mercurial > repos > iuc > bcftools_plugin_setgt
annotate bcftools_plugin_setgt.xml @ 20:681bdf1e22ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author | iuc |
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date | Tue, 16 Jul 2024 17:11:40 +0000 |
parents | a1aad8b559c6 |
children | a730269af659 |
rev | line source |
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7e1a7520e05f
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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 <description>plugin Sets genotypes</description> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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4 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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5 <token name="@EXECUTABLE@">setGT</token> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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6 <token name="@PLUGIN_ID@">setgt</token> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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7 <import>macros.xml</import> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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8 </macros> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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9 <expand macro="bio_tools" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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10 <expand macro="requirements" /> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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11 <expand macro="version_command" /> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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12 <command detect_errors="aggressive"><![CDATA[ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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13 @PREPARE_ENV@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 @PREPARE_INPUT_FILE@ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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15 #set $section = $sec_restrict |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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16 @PREPARE_TARGETS_FILE@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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17 @PREPARE_REGIONS_FILE@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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18 bcftools plugin @EXECUTABLE@ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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19 |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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20 ## VCF input section |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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21 #set $section = $sec_restrict |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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22 @REGIONS@ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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23 @TARGETS@ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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24 |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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25 @OUTPUT_TYPE@ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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26 @THREADS@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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27 |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28 ## Primary Input/Outputs |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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29 @INPUT_FILE@ |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 ## Plugin section |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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32 #set $section = $sec_plugin |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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33 -- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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34 --target-gt '$section.target_gt' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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35 --new-gt '$section.new_gt' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
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36 |
a1aad8b559c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
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37 #set $section = $sec_restrict |
a1aad8b559c6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
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38 @INCLUDE@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
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39 @EXCLUDE@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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40 > '$output_file' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 ]]> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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42 </command> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43 <inputs> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 <expand macro="macro_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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45 <section name="sec_restrict" title="Restrict to"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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46 <expand macro="macro_restrict" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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47 <expand macro="macro_restrict" type="target" label_type="Target" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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48 <expand macro="macro_include" /> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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49 <expand macro="macro_exclude" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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50 </section> |
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51 <section name="sec_plugin" expanded="true" title="Plugin Options"> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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52 <param name="target_gt" type="select" label="Target genotypes to change"> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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53 <option value="./.">./. completely missing (. or ./., depending on ploidy)</option> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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54 <option value="./x">./x partially missing (./0 or .|1)</option> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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55 <option value=".">. partially or completely missing</option> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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56 <option value="a">a all genotypes</option> |
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57 <option value="b">b heterozygous genotypes failing two-tailed binomial test</option> |
40daf124be88
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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58 <option value="q">q select genotypes using -i/-e options</option> |
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59 </param> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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60 <param name="new_gt" type="select" label="New genotypes to set"> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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61 <option value=".">. missing (. or ./., keeps ploidy)</option> |
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62 <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option> |
40daf124be88
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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63 <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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64 <option value="M">M major allele</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
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65 <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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66 <option value="p">p phased genotype</option> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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67 <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option> |
7e1a7520e05f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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68 </param> |
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69 </section> |
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70 <expand macro="macro_select_output_type" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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71 </inputs> |
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72 <outputs> |
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73 <expand macro="macro_vcf_output" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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74 </outputs> |
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75 <tests> |
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76 <test> |
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77 <param name="input_file" ftype="vcf" value="plugin1.vcf" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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78 <param name="target_gt" value="." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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79 <param name="new_gt" value="0" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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80 <param name="output_type" value="v" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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81 <output name="output_file"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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82 <assert_contents> |
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83 <has_text text="0/0:245" /> |
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84 </assert_contents> |
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85 </output> |
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86 </test> |
17
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87 <test> |
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88 <param name="input_file" ftype="vcf" value="plugin1.vcf" /> |
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89 <section name="sec_restrict"> |
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90 <param name="exclude" value="FMT/GQ>20"/> |
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91 </section> |
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92 <section name="sec_plugin"> |
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93 <param name="target_gt" value="q" /> |
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94 <param name="new_gt" value="." /> |
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95 </section> |
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96 <param name="output_type" value="v" /> |
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97 <output name="output_file"> |
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98 <assert_contents> |
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99 <has_text text="DP4=1,2,3,4;INDEL;STR=test" /> |
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100 <has_n_lines n="38"/> |
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101 </assert_contents> |
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102 </output> |
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103 </test> |
0
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104 </tests> |
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105 <help><![CDATA[ |
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106 ===================================== |
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107 bcftools @EXECUTABLE@ plugin |
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108 ===================================== |
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109 |
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110 @REGIONS_HELP@ |
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111 @TARGETS_HELP@ |
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112 @EXPRESSIONS_HELP@ |
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113 |
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114 ]]></help> |
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115 <expand macro="citations" /> |
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116 </tool> |