Mercurial > repos > iuc > colibread_discosnp_pp

annotate discosnp_pp.xml @ 2:496fdb2db9db draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit b24ba669c32dd33efcc60eee595a18abd639ca7a
author iuc
date Wed, 05 Sep 2018 09:02:35 -0400
parents c2d90cc4a063
children 912d042e4f1e
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dc70286127fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <?xml version='1.0' encoding='utf-8'?>
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c2d90cc4a063 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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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>
dc70286127fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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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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c2d90cc4a063 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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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
dc70286127fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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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}' &&
dc70286127fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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24 #end if
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dc70286127fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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26 run_discoSnp++.sh
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c2d90cc4a063 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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27 @discosnp_inputs@
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28 ${t}
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29 ${T}
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30 #if str($VCF_option.mapping) == 'reference'
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31 -G '${reference_file}'
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32 -M ${VCF_option.M}
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33 ${VCF_option.R}
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34 #end if
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36 ]]></command>
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38 <inputs>
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39
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c2d90cc4a063 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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41 <expand macro="discosnp_inputs" />
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43 <param argument="-b" type="select" label="Branching strategy">
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44 <option value="0">variants for which any of the two paths is branching are discarded</option>
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45 <option value="1">forbid SNPs for wich the two paths are branching</option>
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46 <option value="2">No limitation on branching</option>
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47 </param>
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48
1
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49 <expand macro="discosnp_options" />
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51 <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" />
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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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53
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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="-M" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" />
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63 <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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64 </when>
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65 </conditional>
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66
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67 </inputs>
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68
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69 <outputs>
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70 <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
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71 <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
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72 </outputs>
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74 <tests>
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75 <test>
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76 <conditional name="input_type_options">
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77 <param name="input_type" value="single"/>
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78 <param name="list_reads" value="discosnp/reads1,discosnp/reads2" ftype="fasta" />
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79 </conditional>
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80 <param name="k" value="25"/>
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81 <output name="fasta" file="discosnp/multifasta.fa"/>
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82 <output name="vcf" file="discosnp/vcf_file.vcf" compare="diff" lines_diff="2"/>
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83 </test>
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84 <test>
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85 <conditional name="input_type_options">
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86 <param name="input_type" value="paired"/>
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87 <param name="list_paired_reads">
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88 <collection type="list:paired">
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89 <element name="Pair1">
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90 <collection type="paired">
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91 <element name="forward" value="discosnp/reads1" ftype="fasta"/>
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92 <element name="reverse" value="discosnp/reads2" ftype="fasta"/>
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93 </collection>
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94 </element>
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95 </collection>
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96 </param>
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97 </conditional>
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98 <conditional name="VCF_option">
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99 <param name="mapping" value="reference"/>
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100 <param name="G" value="discosnp/reads1" ftype="fasta"/>
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101 </conditional>
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102 <output name="fasta" file="discosnp/multifasta_paired.fa"/>
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103 <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
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104 </test>
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105 </tests>
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106
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107 <help><![CDATA[
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108
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109 **Description**
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110
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111 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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112
0
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113 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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114
0
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115 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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116
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117 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
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118
1
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119 @discosnp_help@
0
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120
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121 ]]></help>
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122 <expand macro="citations">
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123 <expand macro="discosnp_citation" />
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124 </expand>
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125 </tool>