Mercurial > repos > iuc > bcftools_query
annotate bcftools_query.xml @ 7:e0ad88dec40d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author | iuc |
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date | Thu, 21 Feb 2019 16:05:32 -0500 |
parents | 24ff7b989329 |
children | 0770b1203e90 |
rev | line source |
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0
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 <?xml version='1.0' encoding='utf-8'?> |
7
e0ad88dec40d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> |
0
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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4 <macros> |
2fea169065ec
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@">query</token> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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6 <import>macros.xml</import> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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7 </macros> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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8 <expand macro="requirements" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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9 <expand macro="version_command" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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10 <command detect_errors="aggressive"><![CDATA[ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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11 @PREPARE_ENV@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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12 @PREPARE_INPUT_FILES@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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13 #set $section = $sec_restrict |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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14 @PREPARE_TARGETS_FILE@ |
5
24ff7b989329
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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15 @PREPARE_REGIONS_FILE@ |
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2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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16 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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17 bcftools @EXECUTABLE@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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18 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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19 ## Query section |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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20 #set $section = $sec_query |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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21 --format '${section.format}' |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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22 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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23 ${section.allow_undef_tags} |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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24 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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25 ${section.print_header} |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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26 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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27 ## Default section |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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28 #set $section = $sec_restrict |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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29 @INCLUDE@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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30 @EXCLUDE@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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31 @COLLAPSE@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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32 @REGIONS@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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33 @SAMPLES@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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34 @TARGETS@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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35 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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36 ## Primary Input/Outputs |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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37 --vcf-list @INPUT_LIST_FILE@ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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38 > $output_file |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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39 ]]> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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40 </command> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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41 <inputs> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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42 <expand macro="macro_inputs" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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43 <section name="sec_restrict" expanded="false" title="Restrict to"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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44 <expand macro="macro_collapse" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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45 <expand macro="macro_samples" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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46 <expand macro="macro_regions" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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47 <expand macro="macro_targets" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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48 <expand macro="macro_include" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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49 <expand macro="macro_exclude" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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50 </section> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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51 <section name="sec_query" expanded="true" title="Query Options"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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52 <param name="format" type="text" value="" label="Format for Output"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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53 <help> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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54 <![CDATA[ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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55 Example: %CHROM\t%POS\t%REF\t%ALT{0}\n |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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56 ( NOTE TAB: '\t' and new line character: '\n' ) |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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57 ]]> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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58 </help> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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59 <sanitizer sanitize="False"/> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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60 <validator type="empty_field" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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61 </param> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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62 <param name="tsv" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output is tab-delimited" |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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63 help="Fields in your Format are separated by a TAB character: \t"/> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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64 <param name="allow_undef_tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" label="Allow Undefined Tags" |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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65 help="Print "." for undefined tags" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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66 <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header Line" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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67 </section> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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68 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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69 </inputs> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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70 <outputs> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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71 <data name="output_file" format="txt"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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72 <change_format> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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73 <when input="tsv" value="True" format="tabular" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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74 </change_format> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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75 </data> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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76 </outputs> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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77 <tests> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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78 <test> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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79 <param name="input_files" ftype="vcf" value="query.vcf" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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80 <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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81 <param name="tsv" value="True" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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82 <output name="output_file" file="query.out" /> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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83 </test> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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84 </tests> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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85 <help><![CDATA[ |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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86 ===================================== |
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87 bcftools @EXECUTABLE@ |
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88 ===================================== |
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89 |
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90 Extracts fields from VCF/BCF file and prints them in user-defined format |
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91 |
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92 Format: |
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93 |
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94 :: |
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95 |
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96 ``%CHROM`` The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER) |
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97 ``%INFO/TAG`` Any tag in the INFO column |
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98 ``%TYPE`` Variant type (REF, SNP, MNP, INDEL, OTHER) |
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99 ``%MASK`` Indicates presence of the site in other files (with multiple files) |
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100 ``%TAG{INT}`` Curly brackets to subscript vectors (0-based) |
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101 ``%FIRST_ALT`` Alias for %ALT{0} |
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102 ``[]`` The brackets loop over all samples |
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103 ``%GT`` Genotype (e.g. 0/1) |
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104 ``%TBCSQ`` Translated FORMAT/BCSQ. See the csq command above for explanation and examples. |
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105 ``%TGT`` Translated genotype (e.g. C/A) |
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106 ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A) |
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107 ``%LINE`` Prints the whole line |
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108 ``%SAMPLE`` Sample name |
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109 ``%POS0`` POS in 0-based coordinates |
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110 ``%END`` End position of the REF allele |
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111 ``%END0`` End position of the REF allele in 0-based cordinates |
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112 ``\n`` new line |
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113 ``\t`` tab character |
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114 |
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115 |
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116 Examples: |
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117 |
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118 :: |
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119 |
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120 # Print chromosome, position, ref allele and the first alternate allele |
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121 bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz |
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122 |
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123 # Similar to above, but use tabs instead of spaces, add sample name and genotype |
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124 bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz |
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125 |
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126 # Print FORMAT/GT fields followed by FORMAT/GT fields |
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127 bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf |
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128 |
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129 # Make a BED file: chr, pos (0-based), end pos (1-based), id |
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130 bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf |
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131 |
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132 |
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133 @COLLAPSE_HELP@ |
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134 @REGIONS_HELP@ |
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135 @TARGETS_HELP@ |
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136 @EXPRESSIONS_HELP@ |
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137 |
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138 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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139 |
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140 @BCFTOOLS_WIKI@ |
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141 ]]> |
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142 </help> |
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143 <expand macro="citations" /> |
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144 </tool> |