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annotate vapor.xml @ 4:f75101279f85 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
author iuc
date Wed, 16 Nov 2022 13:40:26 +0000
parents e45e2c23ee5f
children
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f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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1 <tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy3" profile="21.05">
0
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2 <description>
4
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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3 Classify Influenza samples from short reads sequence data
0
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4 </description>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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5 <macros>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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6 <token name="@TOOL_VERSION@">1.0.2</token>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">vapor</xref>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>
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f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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13 <!-- gawk only required for circumventing current bug in command line
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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14 tool => remove once fixed (see command section below) -->
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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15 <requirement type="package" version="5.1.0">gawk</requirement>
0
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16 </requirements>
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17 <command detect_errors="exit_code"><![CDATA[
4
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18 #set $total_refs = int($fasta_file.metadata.sequences)
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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19
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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20 ## The next two lines for on the fly uppercasing are a workaround for a bug
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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21 ## in vapor 1.0.2, which caused sequence comparisons to be case-sensitive.
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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22 ## Got fixed upstream in:
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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23 ## https://github.com/connor-lab/vapor/commit/b5ec5857cbf53ed45ca7487dac2b4b85ecfe33ea
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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24 ## but unfortunately no release has been tagged since.
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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25 ## Remove with next release!!
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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26 awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$fasta_file' > ref_upper.fa &&
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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27 #set $fasta_file = 'ref_upper.fa'
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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28
3
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29 #if str($fastq_input.fastq_input_selector) == "paired"
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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30 #set r1_ext = $fastq_input.fastq1.extension
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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31 #set r2_ext = $fastq_input.fastq2.extension
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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32 ln -s '$fastq_input.fastq1' fastq1.$r1_ext &&
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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33 ln -s '$fastq_input.fastq2' fastq2.$r2_ext &&
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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34 #elif str($fastq_input.fastq_input_selector) == "paired_collection"
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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35 #set r1_ext = $fastq_input.fastq_pairs.forward.extension
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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36 #set r2_ext = $fastq_input.fastq_pairs.reverse.extension
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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37 ln -s '$fastq_input.fastq_pairs.forward' fastq1.$r1_ext &&
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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38 ln -s '$fastq_input.fastq_pairs.reverse' fastq2.$r2_ext &&
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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39 #else
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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40 #set r1_ext = $fastq_input.fastq_single.extension
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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41 ln -s '$fastq_input.fastq_single' fastq1.$r1_ext &&
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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42 #end if
0
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43 vapor.py
4
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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44 #if int($return_best_n) > 0
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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45 --return_best_n $return_best_n
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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46 #else
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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47 --return_best_n $total_refs
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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48 #end if
0
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49 #if $output_type == "fasta"
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50 --return_seqs
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51 #end if
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52 -k $opt.kmer_length
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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53 -t $opt.threshold
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54 -c $opt.min_kmer_cov
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55 -m $opt.min_kmer_prop
0
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56 -fa '$fasta_file'
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57 -fq fastq1.$r1_ext
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58 #if str($fastq_input.fastq_input_selector) in ["paired", "paired_collection"]
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59 fastq2.$r2_ext
e45e2c23ee5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949
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60 #end if
4
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61 -f $opt.top_seed_frac
0
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62 > out_file
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63 ]]></command>
0
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64 <inputs>
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65 <param name="fasta_file" format="fasta" type="data" label="Reference sequences" help="Select a multisample fasta dataset with reference sequences to base classification on." />
3
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66 <conditional name="fastq_input">
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67 <param name="fastq_input_selector" type="select" label="Type of sequencing data">
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68 <option value="single">Single-end</option>
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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69 <option value="paired">Paired-end</option>
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70 <option value="paired_collection">Paired-end as collection</option>
3
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71 </param>
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72 <when value="single">
4
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73 <param name="fastq_single" format="fastqsanger,fastqsanger.gz" type="data" label="Sequenced reads" help="Specify the sequenced reads dataset." />
3
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74 </when>
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75 <when value="paired">
4
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76 <param name="fastq1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads" help="Specify the sequenced reads dataset with forward reads."/>
f75101279f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit e0546646548259ccc4cfd65dbb793fc910fea583
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77 <param name="fastq2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads" help="Specify the sequenced reads dataset with reverse reads."/>
3
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78 </when>
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79 <when value="paired_collection">
4
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80 <param name="fastq_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired collection of sequenced reads" help="Select a collection with forward and reverse reads."/>
3
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81 </when>
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82 </conditional>
4
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83 <param name="output_type" type="select" label="Desired output">
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84 <option value="scores" selected="true">Return scores of best matches</option>
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85 <option value="fasta">Return FASTA sequences of best matches</option>
0
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86 </param>
4
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87 <param name="return_best_n" type="integer" min="0" value="1" label="Limit number of reported matches to" help="Determines the maximum number of candidate matches sorted by score that will be reported. Set to zero to get all candidate matches reported." />
0
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88 <section name="opt" title="Optional arguments" expanded="true">
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89 <param argument="-k" name="kmer_length" type="integer" min="5" max="30" value="21" label="Kmer Length" help="Generate k-mers of this length from the reference sequences and the sequenced reads. Note: smaller k-mer sizes come at the cost of decreased specificity and k-mer sizes below 21 have an increased risk of contaminating sequences getting analyzed. Only decrease the default (21) if you know your sample is pure (i.e., sequenced reads represent viral reads only), or if you have increased --threshold sufficiently." />
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90 <param argument="--threshold" type="float" min="0" max="1" value="0.2" label="Read kmer filtering threshold" help="Sequenced reads that don't have at least this proportion of their k-mers matching k-mers generated from the reference sequences will not be considered in the analysis; default: 0.2" />
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91 <param argument="--min_kmer_cov" type="integer" min="1" value="5" label="Coverage threshold for k-mer culling" help="Minimum coverage by sequenced reads for a reference k-mer to be kept during culling; default: 5" />
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92 <param argument="--min_kmer_prop" type="float" min="0" max="1" value="0.1" label="Minimum k-mer proportion" help="Minimum proportion of matching kmers required for queries; default: 0.1" />
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93 <param argument="--top_seed_frac" type="float" min="0" max="1" value="1" label="Fraction of best seeds to extend" help="Of the queries still considered after applying the --min_kmer_prop filter above, the tool will calculate and report scores only for this fraction. Lowering this value leads to shorter runtime because fewer scores will have to be calculated, but also to fewer results getting reported. CAVEAT: this version of the tool will round down the result of applying this parameter so it is possible to end up with zero queries to be considered further. Change only if runtime is an issue!" />
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94 </section>
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95 </inputs>
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96 <outputs>
1
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97 <data name="output_scores" from_work_dir="out_file" format="tabular" label="${tool.name} on ${on_string}: closest reference scores">
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98 <filter>output_type == "scores"</filter>
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99 <actions>
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100 <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
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101 </actions>
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102 </data>
1
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103 <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta">
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104 <filter>output_type == "fasta"</filter>
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105 </data>
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106 </outputs>
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107 <tests>
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108 <test expect_num_outputs="1">
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109 <conditional name="fastq_input">
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110 <param name="fastq_input_selector" value="single" />
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111 <param name="fastq_single" ftype="fastq" value="test_reads.fq" />
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112 </conditional>
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113 <param name="fasta_file" value="HA_sample.fa" />
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114 <output name="output_scores" file="output1.tab" />
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115 </test>
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116 <test expect_num_outputs="1">
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117 <conditional name="fastq_input">
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118 <param name="fastq_input_selector" value="single" />
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119 <param name="fastq_single" ftype="fastq" value="test_reads.fq" />
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120 </conditional>
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121 <param name="fasta_file" value="HA_sample.fa" />
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122 <param name="return_best_n" value="0" />
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123 <output name="output_scores" file="output1_full.tab" />
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124 </test>
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125 <test expect_num_outputs="1">
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126 <conditional name="fastq_input">
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127 <param name="fastq_input_selector" value="paired" />
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128 <param name="fastq1" ftype="fastq" value="test_reads.fq" />
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129 <param name="fastq2" ftype="fastq" value="test_reads2.fq" />
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130 </conditional>
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131 <param name="fasta_file" value="HA_sample.fa" />
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132 <output name="output_scores" file="output2.tab" />
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133 </test>
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134 <test expect_num_outputs="1">
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135 <conditional name="fastq_input">
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136 <param name="fastq_input_selector" value="single" />
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137 <param name="fastq_single" ftype="fastqsanger.gz" value="test_reads.fastqsanger.gz" />
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138 </conditional>
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139 <param name="fasta_file" value="HA_sample.fa" />
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140 <output name="output_scores" file="output1.tab" />
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141 </test>
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142 <test expect_num_outputs="1">
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143 <conditional name="fastq_input">
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144 <param name="fastq_input_selector" value="single" />
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145 <param name="fastq_single" value="test_reads.fq" />
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146 </conditional>
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147 <param name="fasta_file" value="HA_sample.fa" />
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148 <section name="opt">
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149 <param name="kmer_length" value="29" />
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150 <param name="threshold" value="0.5" />
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151 <param name="min_kmer_cov" value="7" />
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152 <param name="min_kmer_prop" value="0.5" />
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153 <param name="top_seed_frac" value="0.5" />
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154 </section>
2
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155 <output name="output_scores" file="output4.tab" />
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156 </test>
3
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157 <test expect_num_outputs="1">
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158 <conditional name="fastq_input">
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159 <param name="fastq_input_selector" value="single" />
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160 <param name="fastq_single" value="test_reads.fq" />
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161 </conditional>
0
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162 <param name="fasta_file" value="HA_sample.fa" />
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163 <param name="output_type" value="fasta" />
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164 <param name="return_best_n" value="3" />
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165 <output name="output_fasta" file="output5.fa" />
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166 </test>
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167 </tests>
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168 <help><![CDATA[
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169 **What it does**
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170
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171 VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.
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172 VAPOR works on a fasta file of full-length reference sequences for a given genome segment and a set of sequenced reads, and attempts to retrieve the reference that is closest to the sequenced strain.
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173
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174 `sub_sample` is not an option here (compared to the tool on GitHub), since you can always build a workflow that preprocesses your reads to a (random) subsample. You can use this output as your reads file for VAPOR.
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175 ]]> </help>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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176 <citations>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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177 <citation type="doi">10.1093/bioinformatics/btz814</citation>
9971bc9dd983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 81874af500338d4ba72ca4d2bb11a628fb405525
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178 </citations>
4
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179 </tool>