Mercurial > repos > iuc > colibread_discosnp_rad

annotate discosnp_RAD.xml @ 3:2af5a5ca9c87 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Mon, 17 Aug 2020 10:37:37 -0400
parents 9ee3bf979757
children 923df36f6592
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool profile="16.04" id="discosnp_rad" name="DiscoSnpRAD" version="@DISCOSNP_VERSION@">
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3 <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</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 ## get the absolute path for short_reads_connector
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22 CONNECTOR_PATH=`which short_read_connector.sh` &&
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23 CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` &&
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25 run_discoSnpRad.sh
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26 @discosnp_inputs@
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27 -S "\$CONNECTOR_DIR"
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28 --max_size_cluster ${max_size_cluster}
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29 -a ${a}
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30 ${high_precision}
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31 --max_missing ${max_missing}
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32 --min_rank ${min_rank}
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34 --max_threads \${GALAXY_SLOTS:-1}
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36 ]]></command>
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38 <inputs>
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40 <expand macro="discosnp_inputs" />
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41
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42 <param argument="--high_precision" type="boolean" checked="false" truevalue="--high_precision" falsevalue="" label="Lower recall / higher precision mode." help="With this parameter no symmetrical crossroads may be traversed during bubble detection (by default up to 5 symmetrical crossroads may be traversed during bubble detection)." />
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44 <param argument="-a" type="integer" label="Maximal size of ambiguity of INDELs" value="20" help="INDELS whose ambiguity is higher than this value are not output"/>
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45
3
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46 <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/>
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48 <param argument="--max_missing" type="float" label="Remove variants with more than this proportion of missing values" value="0.95" help="Default 0.95, removes variants detected in 5% and less populations"/>
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50 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
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51
0
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52 <expand macro="discosnp_options" />
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54 </inputs>
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56 <outputs>
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57 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
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58 <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
0
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59 </outputs>
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61 <tests>
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62 <test>
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63 <conditional name="input_type_options">
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64 <param name="input_type" value="single"/>
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65 <param name="list_reads" value="discosnpRAD/loci_reads" ftype="fasta" />
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66 </conditional>
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67 <param name="D" value="0"/>
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68 <param name="P" value="4"/>
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69 <param name="k" value="31"/>
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70 <param name="b" value="2"/>
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71 <param name="max_size_cluster" value="50"/>
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72 <param name="max_missing" value="0.95"/>
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73 <param name="min_rank" value="0.0"/>
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74 <output name="fasta" file="discosnpRAD/fasta.fa"/>
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75 <output name="vcf">
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76 <assert_contents>
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77 <has_n_lines n="31"/>
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78 <has_text text="Ty=SNP;Rk=0.0;UL=23;UR=39;CL=23;CR=39;Genome=.;Sd=.;Cluster=0;ClSize=2"/>
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79 <has_text text="0/1:84:604,15,604:42,42:0,0"/>
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80 </assert_contents>
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81 </output>
3
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82 <assert_command>
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83 <has_text text="--max_size_cluster 50"/>
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84 <has_text text="--max_missing 0.95"/>
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85 <has_text text="--min_rank 0.0"/>
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86 </assert_command>
0
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87 </test>
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88 </tests>
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89
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90 <help><![CDATA[
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91
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92 **Description**
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93
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94 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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95
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96 DiscoSnpRad uses options specific to RAD-Seq: branching strategy, kind of extensions, abundance threshold, and kind of bubbles to be found.
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97
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98 Moreover, it clusters variants per locus by calling the `discoRAD_finalization.sh` pipeline. Cluster information is reported in the final provided VCF file.
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99
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100 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
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101
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102 @discosnp_help@
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103
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104
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105 ]]></help>
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106 <expand macro="citations">
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107 <expand macro="discosnp_citation" />
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108 </expand>
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109 </tool>