Mercurial > repos > trinity_ctat > ctat_metagenomics
changeset 0:cfb4fc1e820d draft
Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
author | trinity_ctat |
---|---|
date | Thu, 12 Apr 2018 10:26:28 -0400 |
parents | |
children | 1c8d5eb15ed1 |
files | ctat_metagenomics.xml tool-data/ctat_centrifuge_indexes.loc.sample tool_data_table_conf.xml.sample |
diffstat | 3 files changed, 170 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_metagenomics.xml Thu Apr 12 10:26:28 2018 -0400 @@ -0,0 +1,145 @@ +<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[ + python 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> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ctat_centrifuge_indexes.loc.sample Thu Apr 12 10:26:28 2018 -0400 @@ -0,0 +1,15 @@ +# This file lists the locations of CTAT Centrifuge Indexes +# Usually there will only be one index, but it is concievable +# that there could be multiple indexes. +# This file format is as follows +# (white space characters are TAB characters): +# +#<value> <name> <path> +# value is a unique id +# name is the display name +# path is the directory where the index files are stored +# +#ctat_centrifuge_indexes.loc could look like: +# +#p_compressed+h+v CTAT_CentrifugeIndex_p_compressed+h+v /ctat/centrifuge/index/path/p_compressed+h+v +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Apr 12 10:26:28 2018 -0400 @@ -0,0 +1,10 @@ +<tables> + <table name="ctat_genome_ref_libs" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_genome_ref_libs.loc" /> + </table> + <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_centrifuge_indexes.loc" /> + </table> +</tables>