Mercurial > repos > trinity_ctat > ctat_metagenomics
diff ctat_metagenomics.xml @ 0:f92fcdde48fc draft default tip
Upload ctat tools.
author | trinity_ctat |
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date | Tue, 17 Jul 2018 11:47:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_metagenomics.xml Tue Jul 17 11:47:13 2018 -0400 @@ -0,0 +1,109 @@ +<tool id="ctat_metagenomics" name="ctat_metagenomics" version="1.0.0" profile="17.05"> + + <description>Centrifuge classifier for metagenomic sequences (RNA-Seq)</description> + <requirements> + <requirement type="package" version="1.0.3=py27pl5.22.0_2">centrifuge</requirement> + <requirement type="package" version="1.0.1">ctat-metagenomics</requirement> + </requirements> + <command detect_errors="default"> + <![CDATA[ + metagenomics + + --index "${index.fields.path}" + --out_dir "centrifuge" + + #if $format_type.format == "fasta" + --format fasta --unpaired_reads $format_type.fasta_file + #end if + + #if $format_type.format == "fastq" + --format fastq + #if $format_type.read_type.type == "single" + --read_type "single" --unpaired_reads $format_type.read_type.left_fq_single + #end if + + #if $format_type.read_type.type == "paired" + --read_type "paired" --left_fq $format_type.read_type.left_fq --right_fq $format_type.read_type.right_fq + #end if + #end if + + --threads 4 + ]]> + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Error running centrifuge" /> + </stdio> + + <inputs> + + <conditional name="format_type"> + <param name= "format" type="select" label="Choose input format" help="Choose fasta for Trinity assembled reads"> + <option value="fasta" selected="true">FASTA</option> + <option value="fastq" selected="false">FASTQ</option> + </param> + <when value="fasta"> + <param name="fasta_file" type="data" format="fasta" label="Fasta file:" help="Trinity assembled reads in fasta format"/> + </when> + <when value="fastq"> + <conditional name="read_type"> + <param name= "type" type="select" label="Choose read type" help="Choose read type"> + <option value="single" selected="true">SINGLE END DATA</option> + <option value="paired" selected="false">PAIRED END DATA</option> + </param> + <when value="single"> + <param name="left_fq_single" type="data" format="fastq" label="Left_fq:" help="Left fastq"/> + </when> + <when value="paired"> + <param name="left_fq" type="data" format="fastq" label="Left_fq:" help="Left fastq"/> + <param name="right_fq" type="data" format="fastq" label="Right_fq:" help="Right fastq"/> + </when> + </conditional> + </when> + </conditional> + + <param name="index" type="select" label="Choose reference genome index :" help="Select genome index"> + <options from_data_table="ctat_centrifuge_indexes" /> + </param> + + </inputs> + + <outputs> + <data format="txt" name="classification_results" label="Centrifuge classification output" from_work_dir="centrifuge/classification.results.txt"/> + <data format="txt" name="classification_report" label="Centrifuge summary output" from_work_dir="centrifuge/classification.report.txt"/> + <data format="txt" name="kraken_style_report" label="Kraken-style report" from_work_dir="centrifuge/kraken_style_report.txt"/> + </outputs> + + <tests> + <test> + <!-- The following test uses one file that is unpaired reads. + --> + <param name="format" value="fastq" /> + <param name="type" value="single" /> + <param name="left_fq_single" value="centrifuge/SRR2219890_1.adj.fastq" /> + <param name="index" value="/N/dc2/projects/galaxyshared/trinity/dev/Trinity_CTAT/metagenomics/phv" /> + <output name="classification_results" > + <assert_contents> + <has_line_matching expression=".+" /> + <has_line line="readID	seqID	taxID	score	2ndBestScore	hitLength	queryLength	numMatches" /> + </assert_contents> + </output> + <output name="classification_report" file="centrifuge/SRR2219890_1.classification.report.txt" /> + <output name="kraken_style_report" file="centrifuge/SRR2219890_1.kraken_style_report.txt" /> + </test> + </tests> + + <help> +.. class:: infomark + +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. + +For more information: + +https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge + + </help> +<citations> + <citation type="doi">10.1101/gr.210641.116</citation> +</citations> +</tool> +