Mercurial > repos > iuc > ivar_variants

annotate ivar_variants.xml @ 13:4aba3e2f4e00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
author iuc
date Sat, 25 Mar 2023 12:48:32 +0000
parents 6680df7660e1
children 41b0633d0f5d
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1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Call variants from aligned BAM file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$ref' ref.fa &&
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10 ln -s '$input_bam' sorted.bam &&
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11 samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants
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12 -p variants
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13 -q $min_qual
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14 -t $min_freq
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15 #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf"
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16 #if str($gtf) != 'None':
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17 -r ref.fa
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18 -g '$gtf'
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19 #end if
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20 #end if
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21 #if str($output_format.choice) == "vcf" or str($output_format.choice) == "tabular_and_vcf"
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22 && python '${__tool_directory__}/ivar_variants_to_vcf.py'
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23 ${output_format.pass_only}
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24 variants.tsv variants.vcf
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
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29 <param name="ref" type="data" format="fasta" label="Reference"/>
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30 <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/>
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31 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/>
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32 <conditional name="output_format">
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33 <param name="choice" type="select" label="Output format">
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34 <option value="tabular">Tabular (native tool output)</option>
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35 <option value="vcf">VCF</option>
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36 <option value="tabular_and_vcf">Both Tabular and VCF</option>
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37 </param>
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38 <when value="vcf">
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39 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/>
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40 </when>
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41 <when value="tabular_and_vcf">
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42 <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/>
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43 <param name="gtf" argument="-g" optional="true" type="data" format="gff" label="Coordinates of ORFs for optional variant effect prediction" help="Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level. This has no effect on the VCF output."/>
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44 </when>
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45 <when value="tabular">
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46 <param name="gtf" argument="-g" optional="true" type="data" format="gff" label="Coordinates of ORFs for optional variant effect prediction" help="Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level."/>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
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52 <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
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53 <actions>
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54 <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA,POS_AA"/>
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55 </actions>
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56 </data>
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57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
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58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
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64 <param name="ref" value="zika/db/PRV.fa"/>
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65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/>
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66 </test>
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67 <test expect_num_outputs="1">
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68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
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69 <param name="ref" value="zika/db/PRV.fa"/>
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70 <conditional name="output_format">
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71 <param name="choice" value="vcf"/>
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72 </conditional>
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73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/>
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74 </test>
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75 <test expect_num_outputs="2">
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76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
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77 <param name="ref" value="zika/db/PRV.fa"/>
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78 <conditional name="output_format">
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79 <param name="choice" value="tabular_and_vcf"/>
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80 <param name="pass_only" value="true"/>
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81 </conditional>
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82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/>
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83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
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84 </test>
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85 <test expect_num_outputs="1">
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86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
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87 <param name="ref" value="zika/db/PRV.fa"/>
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88 <param name="gtf" value="zika/db/PRV.gff"/>
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89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
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90 </test>
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91 <test expect_num_outputs="2">
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92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
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93 <param name="ref" value="zika/db/PRV.fa"/>
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94 <param name="gtf" value="zika/db/PRV.gff"/>
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95 <conditional name="output_format">
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96 <param name="choice" value="tabular_and_vcf"/>
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97 <param name="pass_only" value="true"/>
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98 </conditional>
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99 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
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100 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 iVar uses the output of the samtools mpileup command to call variants -
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105 single nucleotide variants(SNVs) and indels. In order to call variants
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106 correctly, the reference file used for alignment must be passed to iVar
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107 using the -r flag. The output of samtools pileup is piped into ivar variants
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108 to generate a .tsv file with the variants. There are two parameters that can
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109 be set for variant calling using iVar - minimum quality(Default: 20) and
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110 minimum frequency(Default: 0.03). Minimum quality is the minimum quality for
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111 a base to be counted towards the ungapped depth to canculate iSNV frequency
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112 at a given position. For insertions, the quality metric is discarded and the
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113 mpileup depth is used directly. Minimum frequency is the minimum frequency
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114 required for a SNV or indel to be reported.
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115
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116 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
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117
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118 Optionally output is converted to VCF using a version of the
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119 `ivar_variants_to_vcf.py script <https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py>`_,
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120 that has been modified to store attributes in INFO fields.
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121 ]]></help>
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122 <expand macro="citations">
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123 <citation type="bibtex">@misc{githubivar_variants_to_vcf,
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124 author = {Fernandez, Sarai Varona and Patel, Harshil},
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125 year = {2021},
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126 title = {ivar_variants_to_vcf},
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127 url = {https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py}
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128 }</citation>
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129 </expand>
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130 </tool>