Mercurial > repos > iuc > bcftools_consensus

annotate bcftools_consensus.xml @ 8:70b8e9908ea8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 12:58:42 -0400
parents 2363ef414c9b
children a87ae767b01d
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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="@TOOL_VERSION@+galaxy1">
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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="samtools_requirement"/>
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10 </expand>
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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 = $reference_source
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16 @PREPARE_FASTA_REF@
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18 bcftools @EXECUTABLE@
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19
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20 @FASTA_REF@
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21
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22 ## Default section
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23 #set $section = $sec_default
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25 ${section.iupac_codes}
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27 #if $section.mask:
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28 --mask "${section.mask}"
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29 #end if
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31 #if $section.select_haplotype:
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32 --haplotype "${section.select_haplotype}"
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33 #end if
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34 @SAMPLE@
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35
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36 #if $chain:
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37 --chain "$chain_file"
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38 #end if
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39
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40 ## Primary Input/Outputs
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41 --output "$output_file"
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42 @INPUT_FILE@
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43 ]]>
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44 </command>
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45 <inputs>
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46 <expand macro="macro_input" />
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47 <expand macro="macro_fasta_ref" />
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48 <section name="sec_default" expanded="true" title="Default Options">
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49 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
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50 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes"
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51 help="Output variants in the form of IUPAC ambiguity codes" />
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52 <expand macro="macro_sample" />
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53 <param name="select_haplotype" type="select" optional="true">
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54 <option value="1">1</option>
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55 <option value="2">2</option>
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56 </param>
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57 </section>
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58 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
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59 </inputs>
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60 <outputs>
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61 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
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62 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
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63 <filter>chain</filter>
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64 </data>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <expand macro="test_using_reference" ref="consensus.fa" />
0
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69 <param name="input_file" ftype="vcf" value="consensus.vcf" />
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70 <param name="mask" ftype="tabular" value="consensus.tab" />
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71 <param name="chain" value="True" />
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72 <output name="output_file">
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73 <assert_contents>
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74 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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75 </assert_contents>
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76 </output>
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77 <output name="chain_file">
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78 <assert_contents>
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79 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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80 </assert_contents>
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81 </output>
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82 </test>
8
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83 <test>
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84 <expand macro="test_using_reference" select_from="cached" ref="consensus" />
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85 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
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86 <param name="mask" ftype="tabular" value="consensus.tab" />
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87 <param name="chain" value="True" />
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88 <output name="output_file">
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89 <assert_contents>
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90 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
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91 </assert_contents>
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92 </output>
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93 <output name="chain_file">
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94 <assert_contents>
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95 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
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96 </assert_contents>
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97 </output>
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98 </test>
0
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99 </tests>
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100 <help><![CDATA[
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101 =====================================
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102 bcftools @EXECUTABLE@ plugin
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103 =====================================
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104
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105
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106 Create consensus sequence by applying VCF variants to a reference fasta file.
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107
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108 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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109
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110 @BCFTOOLS_WIKI@
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111 ]]>
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112 </help>
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113 <expand macro="citations" />
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114 </tool>