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planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 969557932bff35913d93068d16facb8da4d64123
author nml
date Thu, 02 Nov 2017 14:09:07 -0400
parents e1867440ed36
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1 <tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.1">
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>
1
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7 <command detect_errors="exit_code"><![CDATA[
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8 perl '$__tool_directory__/seqtk_nml.pl'
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10 --ref '$fastar'
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12 #if $single_or_paired.type == "single"
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13 --type single
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14 --forward '$input_se'
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15 --out_forward '$output'
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16
1
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17 #elif $single_or_paired.type == "paired"
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18 --type paired
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19 --forward '$single_or_paired.forward_pe'
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20 --reverse '$single_or_paired.reverse_pe'
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21 --out_forward '$output'
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22 --out_reverse '$output_rev'
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24 #else
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25 --type paired
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26 --forward '$single_or_paired.fastq_collection.forward'
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27 --reverse '$single_or_paired.fastq_collection.reverse'
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28 --out_forward '$output_collection.forward'
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29 --out_reverse '$output_collection.reverse'
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30 #end if
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31
1
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32 --cov '$coverage'
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33 --log '$log'
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34
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35 ]]></command>
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36 <inputs>
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37 <conditional name="single_or_paired">
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38 <param name="type" type="select" label="Read type">
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39 <option value="single">Single-end</option>
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40 <option value="paired">Paired-end</option>
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41 <option value="collection">Collection Paired-end</option>
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42 </param>
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43 <when value="single">
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44 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
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45 </when>
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46 <when value="paired">
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47 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
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48 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
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49 </when>
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50 <when value="collection">
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51 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
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52 </when>
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53 </conditional>
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54 <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
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55 <param name="coverage" type="integer" label="Desired Coverage" value="50" />
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56 </inputs>
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57 <outputs>
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58 <data format="fastqsanger" name="output" label="SubSampled Fastq" >
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59 <filter>single_or_paired['type']!="collection"</filter>
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60 </data>
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61 <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
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62 <filter>single_or_paired['type']=="paired"</filter>
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63 </data>
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64 <collection name="output_collection" type="paired" label="SubSampled Fastqs">
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65 <data name="forward" format="fastqsanger"/>
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66 <data name="reverse" format="fastqsanger"/>
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67 <filter>single_or_paired['type']=="collection"</filter>
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68 </collection>
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69 <data format="txt" name="log" label="Log file"/>
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70 </outputs>
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71
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72 <tests>
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73 <test>
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74 <param name="type" value="paired" />
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75 <param name="forward_pe" value="inputforward.fastq" />
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76 <param name="reverse_pe" value="inputreverse.fastq" />
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77 <param name="fastar" value="testref.fasta"/>
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78 <param name="coverage" value="50" />
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79 <output name="output" file="outputforward.fastq" />
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80 <output name="output_rev" file="outputreverse.fastq" />
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81 <output name="log" file="lognosample.log" />
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82 </test>
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83 <test>
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84 <param name="type" value="paired" />
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85 <param name="forward_pe" value="inputforward.fastq" />
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86 <param name="reverse_pe" value="inputreverse.fastq" />
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87 <param name="fastar" value="testref.fasta"/>
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88 <param name="coverage" value="25" />
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89 <output name="output" file="outputdownsamepleforward.fastq" />
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90 <output name="output_rev" file="outputdownsameplereverse.fastq" />
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91 <output name="log" file="logdownsample.log" />
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95 ============
0
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96 What it does
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97 ============
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98 Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads.
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99
1
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100 =====
0
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101 Usage
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102 =====
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103
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104 **Parameters**
1
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105 - Fastq reads (single end, paired end, or paired end collection)
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106 - Fasta reference file
0
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107
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108 **Options**
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109 - Desired coverage (50)
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110 ]]></help>
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111 <citations>
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112 <citation type="doi">10.1371/journal.pone.0163962</citation>
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113 </citations>
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114 </tool>