Mercurial > repos > trinity_ctat > ctat_metagenomics

annotate ctat_metagenomics.xml @ 2:e5182440ba17 draft

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Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
author trinity_ctat
date Fri, 13 Apr 2018 14:57:51 -0400
parents 1c8d5eb15ed1
children 983f4f1c7f73
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e5182440ba17 Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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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="1.0.1">ctat-metagenomics</requirement>
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6 </requirements>
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7 <command detect_errors="default">
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8 <![CDATA[
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9 metagenomics.py
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10
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11 --index "${index.fields.path}"
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12 --out_dir "centrifuge"
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13
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14 #if $format_type.format == "fasta"
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15 --format fasta --unpaired_reads $format_type.fasta_file
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16 #end if
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17
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18 #if $format_type.format == "fastq"
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19 --format fastq
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20 #if $format_type.read_type.type == "single"
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21 --read_type "single" --unpaired_reads $format_type.read_type.left_fq_single
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22 #end if
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23
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24 #if $format_type.read_type.type == "paired"
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25 --read_type "paired" --left_fq $format_type.read_type.left_fq --right_fq $format_type.read_type.right_fq
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26 #end if
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27 #end if
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28
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29 --threads 4
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30 ]]>
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31 </command>
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32 <stdio>
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33 <exit_code range="1:" level="fatal" description="Error running centrifuge" />
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34 </stdio>
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35
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36 <inputs>
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37
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38 <conditional name="format_type">
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39 <param name= "format" type="select" label="Choose input format" help="Choose fasta for Trinity assembled reads">
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40 <option value="fasta" selected="true">FASTA</option>
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41 <option value="fastq" selected="false">FASTQ</option>
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42 </param>
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43 <when value="fasta">
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44 <param name="fasta_file" type="data" format="fasta" label="Fasta file:" help="Trinity assembled reads in fasta format"/>
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45 </when>
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46 <when value="fastq">
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47 <conditional name="read_type">
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48 <param name= "type" type="select" label="Choose read type" help="Choose read type">
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49 <option value="single" selected="true">SINGLE END DATA</option>
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50 <option value="paired" selected="false">PAIRED END DATA</option>
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51 </param>
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52 <when value="single">
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53 <param name="left_fq_single" type="data" format="fastq" label="Left_fq:" help="Left fastq"/>
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54 </when>
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55 <when value="paired">
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56 <param name="left_fq" type="data" format="fastq" label="Left_fq:" help="Left fastq"/>
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57 <param name="right_fq" type="data" format="fastq" label="Right_fq:" help="Right fastq"/>
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58 </when>
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59 </conditional>
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60 </when>
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61 </conditional>
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62
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63 <param name="index" type="select" label="Choose reference genome index :" help="Select genome index">
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64 <options from_data_table="ctat_centrifuge_indexes" />
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65 </param>
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66
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67 </inputs>
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68
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69 <outputs>
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70 <data format="txt" name="classification_results" label="Centrifuge classification output" from_work_dir="centrifuge/classification.results.txt"/>
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71 <data format="txt" name="classification_report" label="Centrifuge summary output" from_work_dir="centrifuge/classification.report.txt"/>
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72 <data format="txt" name="kraken_style_report" label="Kraken-style report" from_work_dir="centrifuge/kraken_style_report.txt"/>
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73 </outputs>
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74
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75 <tests>
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76 <test>
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77 <!-- The following test uses one file that is unpaired reads.
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78 -->
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79 <param name="format" value="fastq" />
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80 <param name="type" value="single" />
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81 <param name="left_fq_single" value="centrifuge/SRR2219890_1.adj.fastq" />
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82 <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" />
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83 <output name="classification_results" >
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84 <assert_contents>
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85 <has_line_matching expression=".+" />
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86 <has_line line="readID&#009;seqID&#009;taxID&#009;score&#009;2ndBestScore&#009;hitLength&#009;queryLength&#009;numMatches" />
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87 </assert_contents>
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88 </output>
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89 <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" />
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90 <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" />
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91 </test>
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92 </tests>
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93
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94 <help>
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95 .. class:: infomark
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96
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97 **Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species**
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98
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99 For more information:
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100
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101 https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge
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102
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103 The publication documenting Centrifuge can be found here:
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104
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105 http://genome.cshlp.org/content/early/2016/11/16/gr.210641.116.abstract
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106
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107 </help>
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108 </tool>
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109