Mercurial > repos > iuc > colibread_discosnp_rad

annotate discosnp_RAD.xml @ 5:74ed1718ef58 draft default tip

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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 19:55:43 +0000
parents 923df36f6592
children
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5
74ed1718ef58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
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1 <tool id="discosnp_rad" name="DiscoSnpRAD" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>discovering polymorphism from raw unassembled RADSeq NGS reads.</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 CONNECTOR_PATH=`which short_read_connector.sh` &&
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26 CONNECTOR_DIR=`dirname \$CONNECTOR_PATH` &&
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27 run_discoSnpRad.sh
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28 @discosnp_inputs@
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29 -S "\$CONNECTOR_DIR"
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30 --max_size_cluster ${max_size_cluster}
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31 -a ${a}
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32 ${high_precision}
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33 --max_missing ${max_missing}
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34 --min_rank ${min_rank}
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35 --max_threads \${GALAXY_SLOTS:-1}
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36 ]]></command>
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37 <inputs>
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38 <expand macro="discosnp_inputs" />
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39 <param argument="--high_precision" type="boolean" checked="false" truevalue="--high_precision" falsevalue="" label="Lower recall / higher precision mode." help="With this parameter no symmetrical crossroads may be traversed during bubble detection (by default up to 5 symmetrical crossroads may be traversed during bubble detection)." />
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40 <param argument="-a" type="integer" label="Maximal size of ambiguity of INDELs" value="20" help="INDELS whose ambiguity is higher than this value are not output"/>
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41 <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/>
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42 <param argument="--max_missing" type="float" label="Remove variants with more than this proportion of missing values" value="0.95" help="Default 0.95, removes variants detected in 5% and less populations"/>
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43 <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
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44 <expand macro="discosnp_options" />
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45 </inputs>
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46 <outputs>
5
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47 <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="${tool.name} on ${on_string}: VCF"/>
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48 <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="${tool.name} on ${on_string}: FASTA"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <conditional name="input_type_options">
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53 <param name="input_type" value="single"/>
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54 <param name="list_reads" value="discosnpRAD/loci_reads.gz" ftype="fasta.gz" />
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55 </conditional>
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56 <param name="D" value="0"/>
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57 <param name="P" value="4"/>
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58 <param name="k" value="31"/>
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59 <param name="max_size_cluster" value="50"/>
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60 <param name="max_missing" value="0.95"/>
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61 <param name="min_rank" value="0.0"/>
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62 <output name="fasta" file="discosnpRAD/fasta.fa"/>
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63 <output name="vcf">
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64 <assert_contents>
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65 <has_n_lines n="31"/>
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66 <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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67 <has_text text="0/1:84:604,15,604:42,42:0,0"/>
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68 </assert_contents>
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69 </output>
3
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70 <assert_command>
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71 <has_text text="--max_size_cluster 50"/>
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72 <has_text text="--max_missing 0.95"/>
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73 <has_text text="--min_rank 0.0"/>
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74 </assert_command>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78
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79 **Description**
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80
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81 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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82
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83 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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84
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85 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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86
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87 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
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88
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89 @discosnp_help@
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90
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91
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92 ]]></help>
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93 <expand macro="citations">
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94 <expand macro="discosnp_citation" />
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95 </expand>
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96 </tool>