Mercurial > repos > bhaas > trinityrnaseq
changeset 0:177bb1b443db draft default tip
Uploaded
| author | bhaas |
|---|---|
| date | Mon, 16 Jul 2012 09:18:23 -0400 |
| parents | |
| children | |
| files | trinityrnaseq.xml |
| diffstat | 1 files changed, 127 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinityrnaseq.xml Mon Jul 16 09:18:23 2012 -0400 @@ -0,0 +1,127 @@ +<tool id="trinityrnaseq" name="Trinity" version="0.0.1"> + + <!-- Written by Jeremy Goecks, now maintained here by bhaas --> + <description>De novo assembly of RNA-Seq data Using Trinity</description> + <requirements> + <requirement type="package">trinity</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 $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax + #if $inputs.bfly_opts != 'None': + --bfly_opts " $inputs.bfly_opts " + #end if + #end if + + + ## direct to output + > $trinity_log 2>&1 + + </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> + <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>