Mercurial > repos > iuc > bcftools_plugin_frameshifts

annotate bcftools_plugin_frameshifts.xml @ 16:b05f29f085cf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
author iuc
date Sat, 15 Jan 2022 13:09:53 +0000
parents 0bc62e388dfa
children 50d07d6c1388
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b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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1 <?xml version='1.0' encoding='utf-8'?>
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758ce6301579 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
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b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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3 <description>plugin Annotate frameshift indels</description>
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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4 <macros>
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5 <token name="@EXECUTABLE@">frameshifts</token>
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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6 <token name="@PLUGIN_ID@">frameshifts</token>
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7 <import>macros.xml</import>
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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8 </macros>
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b05f29f085cf "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" />
9
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10 <expand macro="requirements" />
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11 <expand macro="version_command" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 @PREPARE_ENV@
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14 @PREPARE_INPUT_FILE@
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15 #set $section = $sec_restrict
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16 @PREPARE_TARGETS_FILE@
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17 @PREPARE_REGIONS_FILE@
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18 ## exons file needs to be bgzip and have tabix index
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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19 bgzip -c $exons > exons.bed.gz &&
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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20 tabix exons.bed.gz &&
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22 bcftools plugin @EXECUTABLE@
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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23 ## VCF input section
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24 #set $section = $sec_restrict
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25 @INCLUDE@
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26 @EXCLUDE@
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27 @REGIONS@
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28 @TARGETS@
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29
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30 @OUTPUT_TYPE@
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31 @THREADS@
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32
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33 ## Primary Input/Outputs
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34 @INPUT_FILE@
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35 ## Plugin options
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36 -- --exons exons.bed.gz
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37 > '$output_file'
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38 ]]>
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39 </command>
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40 <inputs>
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41 <expand macro="macro_input" />
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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42 <param name="exons" type="data" format="bed"
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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43 label="Exons File" help="BED file describing exons" />
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44 <section name="sec_restrict" expanded="false" title="Restrict to">
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45 <expand macro="macro_restrict" />
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46 <expand macro="macro_restrict" type="target" label_type="Target" />
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47 <expand macro="macro_include" />
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48 <expand macro="macro_exclude" />
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49 </section>
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50 <expand macro="macro_select_output_type" />
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51 </inputs>
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52 <outputs>
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53 <expand macro="macro_vcf_output" />
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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58 <param name="exons" ftype="bed" value="plugin_frameshifts.bed" />
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59 <param name="output_type" value="v" />
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60 <output name="output_file" ftype="vcf">
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61 <assert_contents>
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62 <has_line_matching expression="##INFO=&lt;ID=OOF,.+" />
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63 <has_line_matching expression="1&#09;3106154&#09;.&#09;CAAA&#09;C&#09;.+&#09;.+&#09;OOF=0.+" />
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64 <has_line_matching expression="1&#09;3106154&#09;.&#09;C&#09;CT&#09;.+&#09;.+&#09;OOF=1.+" />
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65 </assert_contents>
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66 </output>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 =====================================
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71 bcftools @EXECUTABLE@ plugin
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72 =====================================
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73
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74 A simple tool to annotate the effect of indel variants.
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75
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76 Adds an ``OOF`` (out-of-frame) subfield to the ``INFO`` field of indel records
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77 found in the input, where
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78
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79 - ``OOF=1`` indicates that the indel results in a frameshift
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80 - ``OOF=0`` indicates an in-frame indel
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81
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82 The information about indel effects is extracted from the ``BED`` input, which
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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83 is supposed to describe the reference genome exons.
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84
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85 If a variant record lists several ``ALT`` alleles, some of them indels, then
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86 ``OOF`` will be a comma-separated list of status indicators. In the list a
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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87 third ``OOF`` status code of ``-1`` will be used to indicate ``ALT`` alleles
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88 that are not associated with a change in sequence length or that don't affect
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89 an exon.
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90
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91 The formal definition (added to the VCF header) of the ``OOF`` subfield is::
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92
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93 INFO=<ID=OOF,Number=A,Type=Integer,Description="Frameshift Indels: out-of-frame (1), in-frame (0), not-applicable (-1 or missing)">
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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94
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95 @REGIONS_HELP@
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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96 @TARGETS_HELP@
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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97 @EXPRESSIONS_HELP@
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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98
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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99 ]]></help>
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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100 <expand macro="citations" />
b14468416547 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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101 </tool>