Mercurial > repos > jjohnson > trinityrnaseq
view trinityrnaseq.xml @ 9:09c1e388c20c default tip
Change samtools tool_dependency to iuc package_samtools_0_1_19
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 06 Feb 2014 10:45:40 -0600 |
parents | d5580071d910 |
children |
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<tool id="trinityrnaseq" name="Trinity" version="0.0.2"> <!-- Written by Jeremy Goecks, now maintained here by bhaas --> <description>De novo assembly of RNA-Seq data Using Trinity</description> <requirements> <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="1.0.0">bowtie</requirement> </requirements> <command> Trinity.pl --JM $JM --CPU $CPU ## Inputs. #if str($inputs.paired_or_single) == "paired": --left $inputs.left_input --right $inputs.right_input #if $inputs.left_input.ext == 'fa': --seqType fa #else: --seqType fq #end if #if str($inputs.library_type) != "None": --SS_lib_type $inputs.library_type #end if --group_pairs_distance $inputs.group_pairs_distance #else: --single $inputs.input #if str($inputs.input.ext) == 'fa': --seqType fa #else: --seqType fq #end if #if str($inputs.library_type) != "None": --SS_lib_type $inputs.library_type #end if #end if ## Additional parameters. #if str($additional_params.use_additional) == "yes": --min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax #if $additional_params.bfly_opts != 'None': --bfly_opts " $additional_params.bfly_opts " #end if #end if ## direct output to the log file | tee $trinity_log ## Check output for success message (direct grep output to dev null, -q option quits early leaving tee error messages) | grep 'All commands completed successfully.' > /dev/null ## Print the stats to output to provide info on galaxy history item && \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta </command> <inputs> <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction"> <option value="1G">1G</option> <option value="10G">10G</option> <option value="50G">50G</option> <option value="100G">100G</option> <option value="200G">200G</option> <option value="500G">500G</option> </param> <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" /> <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="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/> <param name="path_reinforcement_distance" type="integer" value="75" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" /> </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> <param name="path_reinforcement_distance" type="integer" value="40" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" /> </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_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" /> <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" /> <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" /> <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly"> <option value="1G">1G</option> <option value="2G">2G</option> <option value="4G" selected="true">4G</option> <option value="10G">10G</option> <option value="20G">20G</option> </param> <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> </when> </conditional> </inputs> <stdio> <exit_code range="1:" level="fatal" description="Failed" /> <regex match="command not found" source="both" level="fatal" description="Trinity.pl not found" /> </stdio> <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> <test> <param name="JM" value="1G"/> <param name="CPU" value="1"/> <param name="paired_or_single" value="single"/> <param name="input" ftype="fastq" value="reads.left.fq"/> <param name="library_type" value="None"/> <param name="path_reinforcement_distance" value="40"/> <param name="use_additional" value="no"/> <output name="trinity_log"> <assert_contents> <!-- sequence merged from multiple reads --> <has_text text="Butterfly assemblies are written to" /> </assert_contents> </output> <output name="assembled_transcripts"> <assert_contents> <!-- sequence merged from multiple reads --> <has_text text="CCATGAGGGGGGGGGGCAATGG" /> </assert_contents> </output> </test> <test> <param name="JM" value="1G"/> <param name="CPU" value="1"/> <param name="paired_or_single" value="paired"/> <param name="left_input" ftype="fastq" value="reads.left.fq"/> <param name="right_input" ftype="fastq" value="reads.right.fq"/> <param name="library_type" value="None"/> <param name="group_pairs_distance" value="500"/> <param name="path_reinforcement_distance" value="75"/> <param name="use_additional" value="no"/> <output name="trinity_log"> <assert_contents> <!-- sequence merged from multiple reads --> <has_text text="Butterfly assemblies are written to" /> </assert_contents> </output> <output name="assembled_transcripts"> <assert_contents> <!-- sequence merged from multiple reads --> <has_text text="AAGCTGGCCTCAAATTCCTGATCC" /> </assert_contents> </output> </test> </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>