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view tools/ngs_rna/trinity_all.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="trinity_all" name="Trinity" version="0.0.1"> <!-- Run all steps of Trinity-Inchworm, Chrysalis, and Butterfly-in a single step. Wrapper status is alpha. --> <description>De novo assembly of RNA-Seq data</description> <requirements> <requirement type="package">trinity</requirement> </requirements> <command> Trinity.pl ## Additional parameters. #if $additional_params.use_additional == "yes": --min_contig_length $additional_params.min_contig_length #end if ## Inputs. #if $inputs.paired_or_single == "paired": --left $inputs.left_input --right $inputs.right_input #if $inputs.left_input.ext == 'fa': --seqType fa #else: --seqType fq #end if #if $inputs.library_type != 'None': --SS_lib_type $inputs.library_type #end if #else: --single $inputs.input #if $inputs.input.ext == 'fa': --seqType fa #else: --seqType fq #end if #if $inputs.library_type != 'None': --SS_lib_type $inputs.library_type #end if #end if ## CPU and butterfly options. --CPU 4 --run_butterfly --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command> <inputs> <conditional name="inputs"> <param name="paired_or_single" type="select" label="Paired or Single-end data?"> <option value="paired">Paired</option> <option value="single">Single</option> </param> <when value="paired"> <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> <param name="library_type" type="select" label="Strand-specific Library Type"> <option value="None">None</option> <option value="FR">FR</option> <option value="RF">RF</option> </param> <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/> </when> <when value="single"> <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> <param name="library_type" type="select" label="Strand-specific Library Type"> <option value="None">None</option> <option value="F">F</option> <option value="R">R</option> </param> </when> </conditional> <conditional name="additional_params"> <param name="use_additional" type="select" label="Use Additional Params?"> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> </when> <when value="yes"> <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> </when> </conditional> </inputs> <outputs> <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> </outputs> <tests> </tests> <help> Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass. .. _Trinity: http://trinityrnaseq.sourceforge.net </help> </tool>