Mercurial > repos > iuc > colibread_discosnp_pp

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
author iuc
date Sat, 05 Oct 2024 19:53:21 +0000
parents e229f3c510aa
children
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a23f839ae56d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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1 <tool id="discosnp_pp" name="DiscoSnp++" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>is an efficient tool for detecting SNPs without a reference genome.</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.5.4</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="discosnp_requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if str($input_type_options.input_type) == "single":
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10 @discosnp_single_for@
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11 @single_reads@
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12 @discosnp_single_end_for@
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13 #else if str($input_type_options.input_type) == "paired":
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14 @discosnp_paired_for@
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15 @paired_reads@
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16 @discosnp_paired_end_for@
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17 #else:
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18 @discosnp_single_for@
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19 @single_reads@
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20 @discosnp_single_end_for@
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21 @discosnp_paired_for@
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22 @paired_reads@
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23 @discosnp_paired_end_for@
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24 #end if
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25 #if str($VCF_option.mapping) == 'reference':
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26 #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext
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27 ln -sf '${VCF_option.G}' '${reference_file}' &&
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28 #end if
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29 run_discoSnp++.sh
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30 @discosnp_inputs@
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31 ${T}
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32 -b ${b}
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33 #if str($VCF_option.mapping) == 'reference':
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34 -G '${reference_file}'
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35 ${VCF_option.R}
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36 #end if
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37 --max_threads \${GALAXY_SLOTS:-1}
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38 ]]></command>
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39 <inputs>
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40 <expand macro="discosnp_inputs" />
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41 <param argument="-b" type="select" label="Branching strategy">
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42 <option value="0">variants for which any of the two paths is branching are discarded</option>
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43 <option value="1">forbid SNPs for wich the two paths are branching</option>
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44 <option value="2">No limitation on branching</option>
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45 </param>
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46 <expand macro="discosnp_options" />
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47 <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
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48 <conditional name="VCF_option" >
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49 <param name="mapping" type="select" label="VCF option">
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50 <option value="default">Do not use reference genome</option>
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51 <option value="reference">Mapping with a reference genome</option>
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52 </param>
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53 <when value="default"></when>
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54 <when value="reference">
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55 <param argument="-G" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference genome file" />
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56 <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="${tool.name} on ${on_string}: VCF"/>
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62 <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="${tool.name} on ${on_string}: FASTA"/>
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63 </outputs>
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64 <tests>
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65 <test>
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66 <conditional name="input_type_options">
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67 <param name="input_type" value="single"/>
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68 <param name="list_reads" value="discosnp/reads1.gz,discosnp/reads2.gz" ftype="fasta.gz" />
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69 </conditional>
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70 <param name="k" value="25"/>
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71 <output name="fasta" file="discosnp/multifasta.fa"/>
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72 <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>
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73 </test>
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74 <test>
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75 <conditional name="input_type_options">
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76 <param name="input_type" value="paired"/>
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77 <param name="list_paired_reads">
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78 <collection type="list:paired">
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79 <element name="Pair1">
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80 <collection type="paired">
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81 <element name="forward" value="discosnp/reads1.gz" ftype="fasta.gz"/>
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82 <element name="reverse" value="discosnp/reads2.gz" ftype="fasta.gz"/>
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83 </collection>
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84 </element>
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85 </collection>
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86 </param>
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87 </conditional>
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88 <conditional name="VCF_option">
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89 <param name="mapping" value="reference"/>
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90 <param name="G" value="discosnp/reads1.gz" ftype="fasta.gz"/>
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91 </conditional>
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92 <output name="fasta" file="discosnp/multifasta_paired.fa"/>
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93 <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
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94 </test>
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95 </tests>
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96 <help><![CDATA[
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97
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98 **Description**
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99
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100 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
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101
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102 Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
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103
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104 The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.
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105
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106 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
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107
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108 @discosnp_help@
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109
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110 ]]></help>
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111 <expand macro="citations">
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112 <expand macro="discosnp_citation" />
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113 </expand>
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114 </tool>