Mercurial > repos > trinity_ctat > ctat_metagenomics
view ctat_metagenomics.xml @ 1:1c8d5eb15ed1 draft
Making sure tools are up to date.
author | trinity_ctat |
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date | Thu, 12 Apr 2018 10:46:59 -0400 |
parents | cfb4fc1e820d |
children | e5182440ba17 |
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<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="1.0.1">ctat-metagenomics</requirement> </requirements> <command detect_errors="default"> <![CDATA[ metagenomics.py --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> <test> <!-- The following test uses two files that are left/right paired reads. --> <param name="format" value="fastq" /> <param name="type" value="paired" /> <param name="left_fq" value="centrifuge/SRR073747_1.fastq" /> <param name="right_fq" value="centrifuge/SRR073747_2.fastq" /> <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing? <param name="index.fields.path" 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/SRR073747_1_2.classification.report.txt" /> <output name="kraken_style_report" file="centrifuge/SRR073747_1_2.kraken_style_report.txt" /> </test> <test> <!-- The following test uses an unpaired Trinity fasta file. --> <param name="format_type.format" value="fasta" /> <param name="fasta_file" value="centrifuge/TrinitySRR2219890.fasta" /> <!-- FIX - How are we going to set the index value when we don't know what is in the table? How do we find it for testing? <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/TrinitySRR2219890.classification.report.txt" />> <output name="kraken_style_report" file="centrifuge/TrinitySRR2219890.kraken_style_report.txt" /> </test> </tests> <help> .. class:: infomark **Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species** For more information: https://ccb.jhu.edu/software/centrifuge/manual.shtml#what-is-centrifuge The publication documenting Centrifuge can be found here: http://genome.cshlp.org/content/early/2016/11/16/gr.210641.116.abstract </help> </tool>