Mercurial > repos > iuc > colibread_discosnp_rad

annotate discosnp_RAD.xml @ 0:86b6b719e47d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author iuc
date Fri, 24 Nov 2017 12:48:46 -0500
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86b6b719e47d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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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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20
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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 -a ${a}
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29
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30 ]]></command>
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31
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32 <inputs>
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34 <expand macro="discosnp_inputs" />
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35
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36 <param argument="-b" type="select" label="Branching strategy">
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37 <option value="1">forbid SNPs for wich the two paths are branching</option>
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38 <option value="2">No limitation on branching</option>
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39 </param>
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40
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41 <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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42
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43 <expand macro="discosnp_options" />
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44
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45 </inputs>
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46
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47 <outputs>
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48 <data name="vcf" from_work_dir="*_coherent_sorted_with_clusters.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
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49 <data name="fasta" from_work_dir="discoRad_*_coherent.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 <conditional name="input_type_options">
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55 <param name="input_type" value="single"/>
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56 <param name="list_reads" value="discosnpRAD/loci_reads" ftype="fasta" />
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57 </conditional>
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58 <param name="D" value="0"/>
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59 <param name="P" value="4"/>
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60 <param name="k" value="31"/>
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61 <param name="b" value="2"/>
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62 <output name="fasta" file="discosnpRAD/fasta.fa"/>
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63 <output name="vcf" file="discosnpRAD/vcf_file.vcf" compare="diff" lines_diff="2"/>
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64 </test>
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65 </tests>
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66
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67 <help><![CDATA[
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69 **Description**
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71 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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73 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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74
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75 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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76
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77 Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
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78
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79 @discosnp_help@
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80
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81
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82 ]]></help>
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83 <expand macro="citations">
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84 <expand macro="discosnp_citation" />
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85 </expand>
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86 </tool>