Mercurial > repos > trinity_ctat > ctat_metagenomics
comparison ctat_metagenomics.xml @ 0:f92fcdde48fc draft default tip
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author | trinity_ctat |
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date | Tue, 17 Jul 2018 11:47:13 -0400 |
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-1:000000000000 | 0:f92fcdde48fc |
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1 <tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05"> | |
2 | |
3 <description>Centrifuge classifier for metagenomic sequences (RNA-Seq)</description> | |
4 <requirements> | |
5 <requirement type="package" version="1.0.3=py27pl5.22.0_2">centrifuge</requirement> | |
6 <requirement type="package" version="1.0.1">ctat-metagenomics</requirement> | |
7 </requirements> | |
8 <command detect_errors="default"> | |
9 <![CDATA[ | |
10 metagenomics | |
11 | |
12 --index "${index.fields.path}" | |
13 --out_dir "centrifuge" | |
14 | |
15 #if $format_type.format == "fasta" | |
16 --format fasta --unpaired_reads $format_type.fasta_file | |
17 #end if | |
18 | |
19 #if $format_type.format == "fastq" | |
20 --format fastq | |
21 #if $format_type.read_type.type == "single" | |
22 --read_type "single" --unpaired_reads $format_type.read_type.left_fq_single | |
23 #end if | |
24 | |
25 #if $format_type.read_type.type == "paired" | |
26 --read_type "paired" --left_fq $format_type.read_type.left_fq --right_fq $format_type.read_type.right_fq | |
27 #end if | |
28 #end if | |
29 | |
30 --threads 4 | |
31 ]]> | |
32 </command> | |
33 <stdio> | |
34 <exit_code range="1:" level="fatal" description="Error running centrifuge" /> | |
35 </stdio> | |
36 | |
37 <inputs> | |
38 | |
39 <conditional name="format_type"> | |
40 <param name= "format" type="select" label="Choose input format" help="Choose fasta for Trinity assembled reads"> | |
41 <option value="fasta" selected="true">FASTA</option> | |
42 <option value="fastq" selected="false">FASTQ</option> | |
43 </param> | |
44 <when value="fasta"> | |
45 <param name="fasta_file" type="data" format="fasta" label="Fasta file:" help="Trinity assembled reads in fasta format"/> | |
46 </when> | |
47 <when value="fastq"> | |
48 <conditional name="read_type"> | |
49 <param name= "type" type="select" label="Choose read type" help="Choose read type"> | |
50 <option value="single" selected="true">SINGLE END DATA</option> | |
51 <option value="paired" selected="false">PAIRED END DATA</option> | |
52 </param> | |
53 <when value="single"> | |
54 <param name="left_fq_single" type="data" format="fastq" label="Left_fq:" help="Left fastq"/> | |
55 </when> | |
56 <when value="paired"> | |
57 <param name="left_fq" type="data" format="fastq" label="Left_fq:" help="Left fastq"/> | |
58 <param name="right_fq" type="data" format="fastq" label="Right_fq:" help="Right fastq"/> | |
59 </when> | |
60 </conditional> | |
61 </when> | |
62 </conditional> | |
63 | |
64 <param name="index" type="select" label="Choose reference genome index :" help="Select genome index"> | |
65 <options from_data_table="ctat_centrifuge_indexes" /> | |
66 </param> | |
67 | |
68 </inputs> | |
69 | |
70 <outputs> | |
71 <data format="txt" name="classification_results" label="Centrifuge classification output" from_work_dir="centrifuge/classification.results.txt"/> | |
72 <data format="txt" name="classification_report" label="Centrifuge summary output" from_work_dir="centrifuge/classification.report.txt"/> | |
73 <data format="txt" name="kraken_style_report" label="Kraken-style report" from_work_dir="centrifuge/kraken_style_report.txt"/> | |
74 </outputs> | |
75 | |
76 <tests> | |
77 <test> | |
78 <!-- The following test uses one file that is unpaired reads. | |
79 --> | |
80 <param name="format" value="fastq" /> | |
81 <param name="type" value="single" /> | |
82 <param name="left_fq_single" value="centrifuge/SRR2219890_1.adj.fastq" /> | |
83 <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" /> | |
84 <output name="classification_results" > | |
85 <assert_contents> | |
86 <has_line_matching expression=".+" /> | |
87 <has_line line="readID	seqID	taxID	score	2ndBestScore	hitLength	queryLength	numMatches" /> | |
88 </assert_contents> | |
89 </output> | |
90 <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" /> | |
91 <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" /> | |
92 </test> | |
93 </tests> | |
94 | |
95 <help> | |
96 .. class:: infomark | |
97 | |
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. | |
99 | |
100 For more information: | |
101 | |
102 https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge | |
103 | |
104 </help> | |
105 <citations> | |
106 <citation type="doi">10.1101/gr.210641.116</citation> | |
107 </citations> | |
108 </tool> | |
109 |