Mercurial > repos > nml > seqtk_nml

annotate seqtk_nml.xml @ 0:e1867440ed36 draft

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planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author nml
date Tue, 19 Sep 2017 16:37:42 -0400
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0
e1867440ed36 planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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1 <tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0">
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2 <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
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3 <requirements>
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4 <requirement type="package" version="1.2">seqtk</requirement>
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5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Unknown error has occured"/>
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9 </stdio>
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10 <command>
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11 perl $__tool_directory__/seqtk_nml.pl --ref $fastar
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12
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13 #if $single_or_paired.type == "single"
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14 --type single
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15 --forward $input_se
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16 --cov $coverage
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17 --out_forward $output
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18 --log $log
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19 #elif $single_or_paired.type == "paired"
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20 --type paired
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21 --forward $single_or_paired.forward_pe
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22 --reverse $single_or_paired.reverse_pe
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23 --cov $coverage
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24 --out_forward $output
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25 --out_reverse $output_rev
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26 --log $log
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27 #else
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28 collection
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29 $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
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30 $coverage $output_collection.forward $output_collection.reverse
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31 #end if
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32
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33 </command>
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34 <inputs>
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35 <conditional name="single_or_paired">
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36 <param name="type" type="select" label="Read type">
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37 <option value="single">Single-end</option>
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38 <option value="paired">Paired-end</option>
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39 <option value="collection">Collection Paired-end</option>
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40 </param>
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41 <when value="single">
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42 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
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43 </when>
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44 <when value="paired">
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45 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
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46 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
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47 </when>
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48 <when value="collection">
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49 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
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50 </when>
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51 </conditional>
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52 <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
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53 <param name="coverage" type="integer" label="Desired Coverage" value="50" />
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54 </inputs>
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55 <outputs>
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56 <data format="fastqsanger" name="output" label="SubSampled Fastq" >
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57 <filter>single_or_paired['type']!="collection"</filter>
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58 </data>
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59 <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
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60 <filter>single_or_paired['type']=="paired"</filter>
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61 </data>
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62 <collection name="output_collection" type="paired" label="SubSampled Fastqs">
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63 <data name="forward" format="fastqsanger"/>
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64 <data name="reverse" format="fastqsanger"/>
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65 <filter>single_or_paired['type']=="collection"</filter>
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66 </collection>
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67 <data format="txt" name="log" label="Log file"/>
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68 </outputs>
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69
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70 <tests>
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71 <test>
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72 <param name="type" value="paired" />
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73 <param name="forward_pe" value="inputforward.fastq" />
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74 <param name="reverse_pe" value="inputreverse.fastq" />
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75 <param name="fastar" value="testref.fasta"/>
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76 <param name="coverage" value="50" />
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77 <output name="output" file="outputforward.fastq" />
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78 <output name="output_rev" file="outputreverse.fastq" />
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79 <output name="log" file="lognosample.log" />
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80 </test>
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81 <test>
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82 <param name="type" value="paired" />
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83 <param name="forward_pe" value="inputforward.fastq" />
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84 <param name="reverse_pe" value="inputreverse.fastq" />
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85 <param name="fastar" value="testref.fasta"/>
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86 <param name="coverage" value="25" />
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87 <output name="output" file="outputdownsamepleforward.fastq" />
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88 <output name="output_rev" file="outputdownsameplereverse.fastq" />
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89 <output name="log" file="logdownsample.log" />
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90 </test>
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91 </tests>
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92 <help>
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93 What it does
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94 ============
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95
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96 Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads.
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97
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98
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99 Usage
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100 =====
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101
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102 **Parameters**
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103 - Fastq reads (single end, paired end, or paired end collection)
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104 - Fasta reference file
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105
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106 **Options**
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107 - Desired coverage (50)
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108 </help>
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109 <citations>
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110 <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation>
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111 </citations>
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112 </tool>
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113