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1 <tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05">
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2
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3 <description>Centrifuge classifier for metagenomic sequences (RNA-Seq)</description>
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4 <requirements>
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5 <requirement type="package" version="1.0.3=py27pl5.22.0_2">centrifuge</requirement>
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6 <requirement type="package" version="1.0.1">ctat-metagenomics</requirement>
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7 </requirements>
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8 <command detect_errors="default">
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9 <![CDATA[
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10 metagenomics
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11
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12 --index "${index.fields.path}"
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13 --out_dir "centrifuge"
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14
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15 #if $format_type.format == "fasta"
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16 --format fasta --unpaired_reads $format_type.fasta_file
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17 #end if
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18
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19 #if $format_type.format == "fastq"
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20 --format fastq
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21 #if $format_type.read_type.type == "single"
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22 --read_type "single" --unpaired_reads $format_type.read_type.left_fq_single
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23 #end if
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24
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25 #if $format_type.read_type.type == "paired"
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26 --read_type "paired" --left_fq $format_type.read_type.left_fq --right_fq $format_type.read_type.right_fq
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27 #end if
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28 #end if
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29
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30 --threads 4
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31 ]]>
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32 </command>
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33 <stdio>
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34 <exit_code range="1:" level="fatal" description="Error running centrifuge" />
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35 </stdio>
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36
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37 <inputs>
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38
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39 <conditional name="format_type">
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40 <param name= "format" type="select" label="Choose input format" help="Choose fasta for Trinity assembled reads">
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41 <option value="fasta" selected="true">FASTA</option>
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42 <option value="fastq" selected="false">FASTQ</option>
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43 </param>
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44 <when value="fasta">
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45 <param name="fasta_file" type="data" format="fasta" label="Fasta file:" help="Trinity assembled reads in fasta format"/>
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46 </when>
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47 <when value="fastq">
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48 <conditional name="read_type">
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49 <param name= "type" type="select" label="Choose read type" help="Choose read type">
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50 <option value="single" selected="true">SINGLE END DATA</option>
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51 <option value="paired" selected="false">PAIRED END DATA</option>
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52 </param>
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53 <when value="single">
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54 <param name="left_fq_single" type="data" format="fastq" label="Left_fq:" help="Left fastq"/>
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55 </when>
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56 <when value="paired">
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57 <param name="left_fq" type="data" format="fastq" label="Left_fq:" help="Left fastq"/>
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58 <param name="right_fq" type="data" format="fastq" label="Right_fq:" help="Right fastq"/>
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59 </when>
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60 </conditional>
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61 </when>
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62 </conditional>
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63
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64 <param name="index" type="select" label="Choose reference genome index :" help="Select genome index">
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65 <options from_data_table="ctat_centrifuge_indexes" />
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66 </param>
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67
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68 </inputs>
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69
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70 <outputs>
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71 <data format="txt" name="classification_results" label="Centrifuge classification output" from_work_dir="centrifuge/classification.results.txt"/>
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72 <data format="txt" name="classification_report" label="Centrifuge summary output" from_work_dir="centrifuge/classification.report.txt"/>
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73 <data format="txt" name="kraken_style_report" label="Kraken-style report" from_work_dir="centrifuge/kraken_style_report.txt"/>
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74 </outputs>
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75
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76 <tests>
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77 <test>
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78 <!-- The following test uses one file that is unpaired reads.
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79 -->
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80 <param name="format" value="fastq" />
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81 <param name="type" value="single" />
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82 <param name="left_fq_single" value="centrifuge/SRR2219890_1.adj.fastq" />
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83 <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
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84 <output name="classification_results" >
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85 <assert_contents>
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86 <has_line_matching expression=".+" />
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87 <has_line line="readID	seqID	taxID	score	2ndBestScore	hitLength	queryLength	numMatches" />
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88 </assert_contents>
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89 </output>
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90 <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" />
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91 <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" />
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92 </test>
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93 </tests>
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94
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95 <help>
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96 .. class:: infomark
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97
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98 ctat_metagenomics is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). CTAT's metagenomics is a classifier for metagenomic sequences (RNA-Seq) for foreign transcript detection. It leverages Centrifuge, a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species, and Kraken. As well, we are leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU.
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99
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100 For more information:
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101
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102 https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge
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103
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104 </help>
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105 <citations>
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106 <citation type="doi">10.1101/gr.210641.116</citation>
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107 </citations>
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108 </tool>
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109
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