Mercurial > repos > iuc > colibread_discosnp_pp

annotate discosnp_pp.xml @ 4:d3963fe808d1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Fri, 14 Aug 2020 20:56:10 +0000
parents 7fe259133cb0
children e229f3c510aa
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@">
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3 <description>is an efficient tool for detecting SNPs without a reference genome.</description>
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4 <macros>
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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><![CDATA[
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9 ## simple option
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10 #if str( $input_type_options.input_type) == "single"
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11 @discosnp_single_reads@
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12 ## paired option
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13 #else if str( $input_type_options.input_type) == "paired"
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14 @discosnp_paired_reads@
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15 ## mix option
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16 #else
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17 @discosnp_single_reads@
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18 @discosnp_paired_reads@
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19 #end if
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21 #if str($VCF_option.mapping) == 'reference'
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22 #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext
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23 ln -sf '${VCF_option.G}' '${reference_file}' &&
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24 #end if
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26 run_discoSnp++.sh
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27 @discosnp_inputs@
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28 ${T}
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29 -b ${b}
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30 #if str($VCF_option.mapping) == 'reference'
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31 -G '${reference_file}'
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32 ${VCF_option.R}
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33 #end if
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35 --max_threads \${GALAXY_SLOTS:-1}
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37 ]]></command>
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39 <inputs>
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42 <expand macro="discosnp_inputs" />
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44 <param argument="-b" type="select" label="Branching strategy">
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45 <option value="0">variants for which any of the two paths is branching are discarded</option>
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46 <option value="1">forbid SNPs for wich the two paths are branching</option>
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47 <option value="2">No limitation on branching</option>
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48 </param>
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49
1
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50 <expand macro="discosnp_options" />
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52 <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
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54 <conditional name="VCF_option" >
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55 <param name="mapping" type="select" label="VCF option">
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56 <option value="default">Do not use reference genome</option>
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57 <option value="reference">Mapping with a reference genome</option>
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58 </param>
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59 <when value="default"></when>
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60 <when value="reference">
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61 <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
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62 <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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63 </when>
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64 </conditional>
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66 </inputs>
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68 <outputs>
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69 <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
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70 <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
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71 </outputs>
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73 <tests>
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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="single"/>
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77 <param name="list_reads" value="discosnp/reads1,discosnp/reads2" ftype="fasta" />
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78 </conditional>
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79 <param name="k" value="25"/>
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80 <output name="fasta" file="discosnp/multifasta.fa"/>
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81 <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>
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82 </test>
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83 <test>
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84 <conditional name="input_type_options">
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85 <param name="input_type" value="paired"/>
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86 <param name="list_paired_reads">
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87 <collection type="list:paired">
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88 <element name="Pair1">
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89 <collection type="paired">
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90 <element name="forward" value="discosnp/reads1" ftype="fasta"/>
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91 <element name="reverse" value="discosnp/reads2" ftype="fasta"/>
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92 </collection>
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93 </element>
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94 </collection>
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95 </param>
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96 </conditional>
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97 <conditional name="VCF_option">
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98 <param name="mapping" value="reference"/>
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99 <param name="G" value="discosnp/reads1" ftype="fasta"/>
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100 </conditional>
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101 <output name="fasta" file="discosnp/multifasta_paired.fa"/>
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102 <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
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103 </test>
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104 </tests>
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105
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106 <help><![CDATA[
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107
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108 **Description**
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109
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110 Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
1
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111
0
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112 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.
1
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113
0
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114 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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115
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116 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
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117
1
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118 @discosnp_help@
0
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119
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120 ]]></help>
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121 <expand macro="citations">
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122 <expand macro="discosnp_citation" />
0
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123 </expand>
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124 </tool>