Mercurial > repos > nate > trinity_psc
diff trinityrnaseq.xml @ 0:d0c258caafaf draft
Uploaded
| author | nate |
|---|---|
| date | Tue, 01 Sep 2015 16:15:38 -0400 |
| parents | |
| children | 976e99dd3c2b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq.xml Tue Sep 01 16:15:38 2015 -0400 @@ -0,0 +1,120 @@ +<tool id="trinity_psc" name="Trinity" version="0.0.1"> + + <!-- Written by Jeremy Goecks, now maintained here by bhaas and additional + modifications by Nate Coraor --> + <description>(Beta) De novo assembly of RNA-Seq data Using Trinity on PSC's Greenfield</description> + <requirements> + <!-- These are versions available as modules on Greenfield --> + <requirement type="package" version="1.1.1">bowtie</requirement> + <requirement type="package" version="1.1">samtools</requirement> + <requirement type="package" version="jre7">java</requirement> + <requirement type="package" version="2.0.6">trinity</requirement> + </requirements> + <command> + MEM=`expr "\${GALAXY_SLOTS:-15}" \* 50 - 16` ; + Trinity --max_memory "\${MEM}G" + --CPU "\${GALAXY_SLOTS:-16}" + --bflyHeapSpaceMax "\${MEM}G" + + ## 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) != "undefined": + --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) != "undefined": + --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 + #if $additional_params.bfly_opts != 'None': + --bfly_opts " $additional_params.bfly_opts " + #end if + #end if + + ## direct to output + > $trinity_log 2>&1 + + ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar + || (ec=\$? ; cat $trinity_log >&2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec) + + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Program failed" /> + <exit_code range=":-1" level="fatal" description="DRM killed job" /> + </stdio> + <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="undefined">Not set</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="undefined">Not set</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="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> +.. warning:: This version of Trinity, which runs on Greenfield_ at the `Pittsburgh Supercomputing Center`_, is a **beta** version. It may not be possible to rerun the same version of this tool, Trinity itself, or its other dependencies (Bowtie, SAMtools) in the future. **When rerunning this tool on the same data, it should, but cannot be guaranteed to reproduce the exact same results to the level of certainty as other Galaxy tools.** + +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.github.io +.. _Pittsburgh Supercomputing Center: http://www.psc.edu +.. _Greenfield: http://www.psc.edu/index.php/resources-for-users/computing-resources/greenfield + </help> +</tool>