Mercurial > repos > iuc > bbtools_callvariants

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 46992fbb9d79da3d3c45b0c10f2936cf2af2dbcd
author iuc
date Tue, 19 Nov 2024 14:47:48 +0000
parents 7e041c120b96
children
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8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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1 <tool id="bbtools_callvariants" name="BBTools: call variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>in aligned Bam files</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="bio.tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #import os
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11 #if str($ref_source_cond.ref_source) == 'cached'
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12 #set ref = str($ref_source_cond.reference.fields.path)
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13 #else:
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14 #set ref = $ref_source_cond.reference
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15 #end if
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16
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17 ## callvariants uses the file extension to determine the input format.
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18 #set input_name = str($os.path.basename($input.file_name)) + '.bam'
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19 ln -s '${input}' '${input_name}' &&
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21 callvariants.sh in='${input_name}' threads=\${GALAXY_SLOTS:-4} ref='${ref}' ploidy=$ploidy
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22 #if $output_variant_score_hist:
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23 shist='$output_scorehist'
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24 #end if
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25 #if $output_zygosity_hist:
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26 zhist='$output_zygosityhist'
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27 #end if
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28 #if $output_quality_hist:
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29 qhist='$output_qualityhist'
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30 #end if
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31 #if str($output_format) == 'vcf':
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32 vcf='out.vcf' && mv 'out.vcf' '$output'
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33 #elif str($output_format) == 'gff':
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34 outgff='out.gff' && mv 'out.gff' '$output'
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35 #else:
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36 out='output.txt' && mv 'output.txt' '$output'
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/>
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41 <expand macro="reference_source_cond"/>
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42 <param name="ploidy" type="integer" min="1" value="1" label="Ploidy" help="See help section below"/>
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43 <param name="output_format" type="select" label="Select output format">
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44 <option value="vcf" selected="true">vcf</option>
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45 <option value="gff">gff</option>
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46 <option value="txt">txt</option>
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47 </param>
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48 <param name="output_variant_score_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output variant score histogram?"/>
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49 <param name="output_zygosity_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output zygosity histogram?"/>
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50 <param name="output_quality_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output quality histogram?"/>
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51 </inputs>
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52 <outputs>
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53 <data name="output" format="vcf">
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54 <change_format>
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55 <when input="output_format" value="gff" format="gff"/>
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56 <when input="output_format" value="txt" format="txt"/>
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57 </change_format>
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58 </data>
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59 <data name="output_scorehist" format="tabular" label="${tool.name} on ${on_string} (scorehist)">
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60 <filter>output_variant_score_hist</filter>
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61 </data>
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62 <data name="output_zygosityhist" format="tabular" label="${tool.name} on ${on_string} (zygosityhist)">
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63 <filter>output_zygosity_hist</filter>
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64 </data>
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65 <data name="output_qualityhist" format="tabular" label="${tool.name} on ${on_string} (qualityhist)">
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66 <filter>output_quality_hist</filter>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <test expect_num_outputs="4">
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71 <param name="input" value="cv_input.bam" ftype="bam"/>
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72 <param name="ploidy" value="2"/>
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73 <param name="output_variant_score_hist" value="yes"/>
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74 <param name="output_zygosity_hist" value="yes"/>
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75 <param name="output_quality_hist" value="yes"/>
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76 <output name="output" file="cv_output.vcf" ftype="vcf" compare="diff" lines_diff="4"/>
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77 <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/>
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78 <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/>
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79 <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/>
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80 </test>
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81 <test expect_num_outputs="1">
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82 <param name="input" value="cv_input.bam" ftype="bam"/>
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83 <param name="ploidy" value="2"/>
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84 <param name="output_format" value="gff"/>
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85 <output name="output" file="cv_output.gff" ftype="gff" compare="contains" lines_diff="2"/>
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86 </test>
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87 <test expect_num_outputs="1">
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88 <param name="input" value="cv_input.bam" ftype="bam"/>
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89 <param name="ploidy" value="2"/>
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90 <param name="output_format" value="txt"/>
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91 <output name="output" file="cv_output.txt" ftype="txt" compare="contains" lines_diff="2"/>
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92 </test>
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93 </tests>
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94 <help>
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95 **What it does**
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96
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97 CallVariants is a high-speed, multithreaded variant caller that accepts bam files, and output VCF files. It is capable
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98 of indel realignment, multi-sample variant-calling, and processing samples with arbitrary ploidy.
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99
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100 BBMap is the recommended mapping program for CallVariants, but output from any aligner is acceptable. Reads can be
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101 realigned with the "realign" flag. This is slower, but is highly recommended if the input is from any mapping tool
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102 other than BBMap. Output from BBMap should not be realigned.
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103
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104 **Options**
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105
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106 * **Ploidy** - Arbitrary ploidy is supported - the default is 1 which works for haploid organisms. Allele fractions lower than those expected for the ploidy (for example, anything below 0.5 for a diploid, or 0.25 for a tetraploid) will incur a score penalty. When calling variants on non-haploid organisms, it is crucial to set the ploidy.
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107
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108 </help>
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109 <expand macro="citations"/>
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110 </tool>