Mercurial > repos > iuc > ucsc_fatovcf

annotate fatovcf.xml @ 3:18c9f51a37a1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf commit cf03c3f6b7afb8e673cc5ced6178d4f6f96a9116
author iuc
date Tue, 03 Dec 2024 09:45:26 +0000
parents d49aa685f7f6
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02e7428386ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf commit 16910aa7b33e5ff73430be1ca9d7727f4ea5786a
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1 <tool id="fatovcf" name="faToVcf" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
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2 <description>
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3 Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs
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4 </description>
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5 <macros>
3
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6 <token name="@TOOL_VERSION@">473</token>
0
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-fatovcf</requirement>
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13 </requirements>
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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15 <command detect_errors="exit_code"><![CDATA[
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16 #if $in_fasta
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17 ln -s '$in_fasta' in.fa &&
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18 #end if
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19 faToVcf
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20 in.fa
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21 '$out'
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22 #if $ref_seq.refSeq == "customRef"
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23 -ref=$ref_seq.ref
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24 #end if
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25 $ambiguous
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26 #if $excl_seq.excludeFile
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27 -excludeFile='$excl_seq.excludeFile'
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28 #end if
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29 -maxDiff=$excl_seq.maxDiff
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30 #if $mask_sites.maskSites
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31 -maskSites='$mask_sites.maskSites'
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32 #end if
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33 #if $mask_sites.windowSize > 0
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34 -windowSize=$mask_sites.windowSize
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35 -minAmbigInWindow=$mask_sites.minAmbigInWindow
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36 #end if
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37 $includeNoAltN
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38 -minAc=$minAc
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39 -minAf=$minAf
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40 #if $output.startOffset > 0
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41 -startOffset=$output.startOffset
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42 #end if
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43 $output.includeRef
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44 $output.noGenotypes
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45 #if $output.vcfChrom
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46 -vcfChrom='$output.vcfChrom'
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47 #end if
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48 ]]></command>
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49 <inputs>
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50 <param name="in_fasta" format="fasta" type="data" label="FASTA Alignment" help="Must contain a series of sequences with different names and the same length. Both N and - are treated as missing information." />
2
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51
0
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52 <conditional name="ref_seq">
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53 <param name="refSeq" type="select" label="Determine reference sequence" help="Which sequence from the FASTA file should be used as the reference sequence.">
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54 <option value="" selected="true">Use the first sequence as reference</option>
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55 <option value="customRef">Use a different sequence as reference</option>
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56 </param>
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57 <when value="customRef">
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58 <param argument="-ref" type="text" label="Name of sequence that should be used as reference sequence:" help="Must be present in the FASTA file." />
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59 </when>
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60 <when value="" />
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61 </conditional>
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62
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63 <param name="ambiguous" type="select" label="Treat ambiguous bases" help="If 1: Treat ambiguous bases as N, ambiguous bases (N, R, V etc.) are treated as N (no call). If 2: Resolve ambiguous characters, if the character represents two bases and one is the reference base, convert it to the non-reference base. Otherwise convert it to N. Default: 0: Don't treat ambiguous bases">
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64 <option value="" selected="true">0: Don't treat ambiguous bases</option>
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65 <option value="-ambiguousToN">1: Treat ambiguous bases as N (no call)</option>
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66 <option value="-resolveAmbiguous">2: Resolve ambiguous characters (convert)</option>
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67 </param>
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68
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69 <section name="excl_seq" title="Exclude sequences" expanded="true">
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70 <param argument="-excludeFile" format="txt" type="data" optional="true" label="Exclude sequences from text file" help="Exclude sequences named in file which has one sequence name per line." />
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71 <param argument="-maxDiff" type="integer" min="0" value="0" label="Maximum number of mismatches" help="Exclude sequences with more than N mismatches with the reference sequence. If -windowSize is used, sequences are masked accordingly before the mismatches are counted. Default: 0" />
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72 </section>
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73
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74 <section name="mask_sites" title="Mask sites" expanded="true">
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75 <param argument="-maskSites" format="vcf" type="data" optional="true" label="Mask sites at given positions (VCF file)" help="Exclude variants in positions recommended for masking in file. Typically https://github.com/W-L/ProblematicSites_SARS-CoV2/raw/master/problematic_sites_sarsCov2.vcf" />
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76 <param argument="-windowSize" type="integer" min="0" value="0" label="Window size to mask bases" help="Mask any base for which there are at least -minAmbigWindow bases in a window of +-N bases around the base. Masking approach adapted from https://github.com/roblanf/sarscov2phylo/blob/master/scripts/mask_seq.py Use -windowSize=7 for same results. Default: 0" />
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77 <param argument="-minAmbigInWindow" type="integer" min="1" value="2" label="Minimum of ambiguous characters within the window given above" help="When -windowSize is provided, mask any base for which there are at least this many N, ambiguous or gap characters within the window. Default: 2" />
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78 </section>
2
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79
0
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80 <param argument="-includeNoAltN" type="boolean" truevalue="-includeNoAltN" falsevalue="" label="Include positions without defined ALT allele" help="Include base positions with no alternate alleles observed, but at least one N (missing base/no-call). Default: false" />
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81 <param argument="-minAc" type="integer" min="0" value="0" label="Minimum allele count" help="Ignore alternate alleles observed fewer than N times. Default: 0" />
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82 <param argument="-minAf" type="float" min="0.0" max="1.0" value="0.0" label="Minimum allele frequency" help="Ignore alternate alleles observed in less than F of non-N bases. Default: 0.0" />
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83
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84 <section name="output" title="Output VCF options" expanded="true">
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85 <param argument="-startOffset" type="integer" min="0" value="0" label="Start offset" help="Add N bases to each position, e.g. for trimmed alignments. Default: 0" />
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86 <param argument="-includeRef" type="boolean" truevalue="-includeRef" falsevalue="" label="Include the reference in the genotype columns" help="Default: omitted as redundant (false)" />
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87 <param argument="-noGenotypes" type="boolean" truevalue="-noGenotypes" falsevalue="" label="Output 8-column VCF" help="VCF without the sample genotype columns. Default: false" />
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88 <param argument="-vcfChrom" type="text" optional="true" label="Use this sequence for the CHROM column in the VCF" help="Default: name of the reference sequence." />
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89 </section>
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90 </inputs>
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91 <outputs>
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92 <data name="out" format="vcf" />
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93 </outputs>
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94 <tests>
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95 <test expect_num_outputs="1"> <!-- default params -->
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96 <param name="in_fasta" value="input.fa" />
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97 <output name="out" ftype="vcf" file="out1.vcf" lines_diff="4" />
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98 </test>
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99 <test expect_num_outputs="1"> <!-- set a value for every input parameter-->
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100 <param name="in_fasta" value="input.fa" />
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101
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102 <conditional name="ref_seq">
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103 <param name="refSeq" value="customRef" />
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104 <param name="ref" value="sample3" />
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105 </conditional>
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106
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107 <param name="ambiguous" value="-ambiguousToN" />
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108
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109 <section name="excl_seq">
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110 <param name="excludeFile" value="excl.txt" />
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111 <param name="maxDiff" value="3" />
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112 </section>
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113
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114 <section name="mask_sites">
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115 <param name="maskSites" value="mask.vcf" />
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116 <param name="windowSize" value="7" />
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117 <param name="minAmbigInWindow" value="3" />
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118 </section>
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119
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120 <param name="includeNoAltN" value="true" />
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121 <param name="minAc" value="1" />
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122 <param name="minAf" value="0.1" />
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123
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124 <section name="output">
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125 <param name="startOffset" value="1" />
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126 <param name="includeRef" value="true" />
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127 <param name="noGenotypes" value="true" />
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128 <param name="vcfChrom" value="sample1" />
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129 </section>
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130
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131 <output name="out" ftype="vcf" file="out2.vcf" lines_diff="4" />
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132 </test>
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133 </tests>
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134 <help><![CDATA[
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135 **What it does**
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136
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137 `faToVcf`_ is a tool to extract a VCF from a multi-sequence FASTA alignment.
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138
2
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139 For implementation details see faToVcf's `source code`_.
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140
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141 .. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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142 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/faToVcf/faToVcf.c
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143
0
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144 ]]> </help>
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145 <citations>
1
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146 <citation type="doi">10.1093/bib/bbs038</citation>
0
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147 </citations>
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148 </tool>