Mercurial > repos > iuc > bcftools_norm
annotate bcftools_norm.xml @ 5:e49eeb4059e0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author | iuc |
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date | Thu, 13 Apr 2017 17:42:48 -0400 |
parents | 660f8eec689d |
children | 19905c025d2a |
rev | line source |
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0
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
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1 <?xml version='1.0' encoding='utf-8'?> |
4
660f8eec689d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> |
0
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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3 <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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4 <macros> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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5 <token name="@EXECUTABLE@">norm</token> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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6 <import>macros.xml</import> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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7 </macros> |
4
660f8eec689d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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8 <expand macro="requirements"> |
5
e49eeb4059e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
4
diff
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9 <expand macro="samtools_requirement"/> |
4
660f8eec689d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
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10 </expand> |
0
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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11 <expand macro="version_command" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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12 <command detect_errors="aggressive"><![CDATA[ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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13 @PREPARE_ENV@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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14 @PREPARE_INPUT_FILE@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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15 #set $section = $sec_ref |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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16 @PREPARE_FASTA_REF@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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17 #set $section = $sec_restrict |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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18 @PREPARE_TARGETS_FILE@ |
5
e49eeb4059e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
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19 @PREPARE_REGIONS_FILE@ |
0
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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20 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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21 bcftools @EXECUTABLE@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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22 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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23 #set $section = $sec_ref |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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24 @FASTA_REF@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
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25 ${section.do_not_normalize} |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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26 #if $section.check_ref: |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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27 --check-ref "${section.check_ref}" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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28 #end if |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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29 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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30 ## Default section |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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31 #set $section = $sec_default |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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32 #if $section.rm_dup: |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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33 --rm-dup "${section.rm_dup}" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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34 #end if |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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35 #if $section.multiallelics: |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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36 #set $mtype = '' |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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37 #if $section.multiallelic_types: |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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38 #set $mtype = $section.multiallelic_types |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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39 #end if |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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40 --multiallelics "${section.multiallelics}${mtype}" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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41 #end if |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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42 ${section.strict_filter} |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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43 #if $section.site_win: |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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44 --site-win "${section.site_win}" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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45 #end if |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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46 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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47 #set $section = $sec_restrict |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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48 @REGIONS@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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49 @TARGETS@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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50 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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51 @OUTPUT_TYPE@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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52 @THREADS@ |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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53 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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54 ## Primary Input/Outputs |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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55 @INPUT_FILE@ |
5
e49eeb4059e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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56 > '$output_file' |
0
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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57 ]]> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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58 </command> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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59 <inputs> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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60 <expand macro="macro_input" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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61 <section name="sec_restrict" expanded="false" title="Restrict to"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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62 <expand macro="macro_regions" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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63 <expand macro="macro_targets" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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64 </section> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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65 <section name="sec_ref" expanded="false" title="Reference Options"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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66 <expand macro="macro_fasta_ref" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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67 <param name="check_ref" type="select" label="Check REF" optional="true" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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68 help="What to do when incorrect or missing REF allele is encountered"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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69 <option value="e">check REF alleles and exit (e)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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70 <option value="w">warn (w)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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71 <option value="x">exclude (x)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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72 <option value="s">set bad sites (s)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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73 <option value="wx">warn and exclude (wx)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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74 <option value="ws">warn and set bad sites (ws)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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75 </param> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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76 <param name="do_not_normalize" type="boolean" truevalue="--do-not-normalize" falsevalue="" label="Skip Normalization, just set REF allele" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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77 help="Do not normalize indels, just fix or set the REF allele from the reference (-N, --do-not-normalize with -m or -c s)" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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78 </section> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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79 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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80 <section name="sec_default" expanded="false" title="Default Options"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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81 <param name="rm_dup" type="select" label="Rm Dup" optional="true" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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82 help="Remove duplicate snps|indels|both|any"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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83 <option value="snps">snps</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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84 <option value="indels">indels</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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85 <option value="both">both</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
|
86 <option value="any">any</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
|
87 </param> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
|
88 <param name="multiallelics" type="select" label="~multiallelics" optional="true"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
|
89 <option value="-">split multiallelic sites into biallelic records (-)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
90 <option value="+">join biallelic sites into multiallelic records (+)</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
91 </param> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
|
92 <param name="multiallelic_types" type="select" label="variant types which should be split or merged" optional="true"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
|
93 <option value="snps">snps - only SNP records should be split or merged</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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94 <option value="indels">indels - only indel records should be split or merged</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
|
95 <option value="both">both - records should be split or merged</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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96 <option value="any">any - SNPs and indels should be merged into a single record</option> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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97 </param> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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98 <param name="strict_filter" type="boolean" truevalue="--strict-filter" falsevalue="" label="Strict Filter" |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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99 help="When merging (-m+), merged site is PASS only if all sites being merged PASS" /> |
2
d110fb275304
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
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0
diff
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100 <param name="site_win" type="integer" label="Site Window" value="1000" optional="True" |
0
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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101 help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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102 </section> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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103 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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104 <expand macro="macro_select_output_type" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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105 </inputs> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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106 <outputs> |
e9555e894608
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iuc
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107 <expand macro="macro_vcf_output"/> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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108 </outputs> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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109 <tests> |
e9555e894608
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iuc
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110 <test> |
e9555e894608
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iuc
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111 <param name="input_file" ftype="vcf" value="norm.vcf" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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112 <param name="fasta_ref" ftype="fasta" value="norm.fa" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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113 <param name="output_type" value="v" /> |
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114 <output name="output_file"> |
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115 <assert_contents> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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116 <has_text text="T,TAACCCTA" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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117 <not_has_text text="TAA,TAACCCTAAA" /> |
e9555e894608
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iuc
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118 </assert_contents> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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119 </output> |
e9555e894608
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iuc
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120 </test> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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121 |
e9555e894608
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iuc
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122 <test> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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123 <param name="input_file" ftype="vcf" value="norm.split.vcf" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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124 <param name="multiallelics" value="-" /> |
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125 <param name="output_type" value="v" /> |
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126 <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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127 <assert_contents> |
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128 <not_has_text text="TAA,TAACCCTAAA" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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129 <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAA\t"/> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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130 <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAACCCTAAA\t"/> |
e9555e894608
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131 </assert_contents> |
e9555e894608
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132 </output> |
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iuc
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133 </test> |
e9555e894608
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134 |
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iuc
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135 <test> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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136 <param name="input_file" ftype="vcf" value="norm.split.vcf" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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137 <param name="fasta_ref" ftype="fasta" value="norm.fa" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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138 <param name="multiallelics" value="-" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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139 <param name="output_type" value="v" /> |
e9555e894608
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iuc
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140 <output name="output_file"> |
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141 <assert_contents> |
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142 <not_has_text text="TAA,TAACCCTAAA" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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143 <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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144 <has_text_matching expression="1\t105\t.\tTA\tT\t"/> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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145 </assert_contents> |
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iuc
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146 </output> |
e9555e894608
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iuc
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147 </test> |
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148 |
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149 <test> |
e9555e894608
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iuc
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150 <param name="input_file" ftype="vcf" value="norm.merge.vcf" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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151 <param name="multiallelics" value="+" /> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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152 <param name="output_type" value="v" /> |
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153 <output name="output_file"> |
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154 <assert_contents> |
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155 <has_text text="TAA,TAACCCTAAA" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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156 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tFAIL"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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157 </assert_contents> |
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158 </output> |
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iuc
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159 </test> |
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iuc
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160 <test> |
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iuc
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161 <param name="input_file" ftype="vcf" value="norm.merge.vcf" /> |
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162 <param name="multiallelics" value="+" /> |
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163 <param name="strict_filter" value="true" /> |
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iuc
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164 <param name="output_type" value="v" /> |
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165 <output name="output_file"> |
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166 <assert_contents> |
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167 <has_text text="TAA,TAACCCTAAA" /> |
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168 <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tPASS"/> |
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169 </assert_contents> |
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170 </output> |
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iuc
parents:
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171 </test> |
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172 |
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173 <test> |
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174 <param name="input_file" ftype="vcf" value="norm.setref.vcf" /> |
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175 <param name="fasta_ref" ftype="fasta" value="norm.fa" /> |
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176 <param name="do_not_normalize" value="true" /> |
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177 <param name="check_ref" value="s" /> |
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178 <param name="output_type" value="v" /> |
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179 <output name="output_file"> |
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180 <assert_contents> |
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181 <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/> |
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182 <has_text_matching expression="2\t105\t.\tT\t<DEL>\t999\tPASS"/> |
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183 </assert_contents> |
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184 </output> |
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185 </test> |
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186 |
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187 </tests> |
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188 <help><![CDATA[ |
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189 ===================================== |
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190 bcftools @EXECUTABLE@ |
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191 ===================================== |
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192 |
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193 |
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194 Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows. |
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195 |
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196 @REGIONS_HELP@ |
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197 @TARGETS_HELP@ |
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198 |
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199 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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200 |
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201 @BCFTOOLS_WIKI@ |
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202 ]]> |
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203 </help> |
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204 <expand macro="citations" /> |
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205 </tool> |