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annotate bcftools_consensus.xml @ 1:201536a80600 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:34:31 -0400
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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3 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">consensus</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 @PREPARE_ENV@
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12 @PREPARE_INPUT_FILE@
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13 #set $section = $sec_default
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14 @PREPARE_FASTA_REF@
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16 bcftools @EXECUTABLE@
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17
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18 ## Default section
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19 #set $section = $sec_default
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20 @FASTA_REF@
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21
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22 ${section.iupac_codes}
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23
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24 #if $section.mask:
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25 --mask "${section.mask}"
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26 #end if
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28 #if $section.select_haplotype:
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29 --haplotype "${section.select_haplotype}"
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30 #end if
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31 @SAMPLE@
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32
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33 #if $chain:
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34 --chain "$chain_file"
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35 #end if
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36
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37 ## Primary Input/Outputs
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38 --output "$output_file"
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39 @INPUT_FILE@
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40 ]]>
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41 </command>
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42 <inputs>
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43 <expand macro="macro_input" />
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44 <section name="sec_default" expanded="true" title="Default Options">
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45 <expand macro="macro_fasta_ref" />
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46 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
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47
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48 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes"
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49 help="Output variants in the form of IUPAC ambiguity codes" />
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50 <expand macro="macro_sample" />
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51 <param name="select_haplotype" type="select" optional="true">
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52 <option value="1">1</option>
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53 <option value="2">2</option>
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54 </param>
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55 </section>
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56 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
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57 </inputs>
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58 <outputs>
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59 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
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60 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
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61 <filter>chain</filter>
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62 </data>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="reference_fasta" ftype="fasta" value="consensus.fa" />
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67 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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68 <param name="mask" ftype="tabular" value="consensus.tab" />
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69 <param name="chain" value="True" />
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70 <output name="output_file">
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71 <assert_contents>
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72 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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73 </assert_contents>
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74 </output>
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75 <output name="chain_file">
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76 <assert_contents>
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77 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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78 </assert_contents>
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79 </output>
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80 <output name="chain_file" file="consensus.1.chain" />
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81 </tests>
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82 <help><![CDATA[
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83 =====================================
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84 bcftools @EXECUTABLE@ plugin
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85 =====================================
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86
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87
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88 Create consensus sequence by applying VCF variants to a reference fasta file.
201536a80600 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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89
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90 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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91
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92 @BCFTOOLS_WIKI@
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93 ]]>
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94 </help>
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95 <expand macro="citations" />
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96 </tool>