Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 4:a40a7ffdf14a draft
Uploaded
author | gkumar09 |
---|---|
date | Wed, 23 Sep 2015 15:21:33 -0400 |
parents | 97ddd78dfa8f |
children | 0fba4f817c44 |
files | align_and_estimate_abundance.xml |
diffstat | 1 files changed, 90 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_and_estimate_abundance.xml Wed Sep 23 15:21:33 2015 -0400 @@ -0,0 +1,90 @@ +<tool id="RSEM_abundance_estimation" name="RSEM_abundance_estimation" version="0.0.1"> + + <description>run RSEM to estimate transcript abundances</description> + <requirements> + <requirement type="package">trinity</requirement> + </requirements> + <command interpreter="python"> + + trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference + + ## Inputs. + #if str($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 + + #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 $inputs.library_type + #end if + #end if + + + </command> + <inputs> + <param format="fasta" name="transcripts" type="data" label="transcripts_fasta" help="Fasta sequences for which reads are aligned." /> + + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <when value="paired"> + <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="FR">FR</option> + <option value="RF">RF</option> + </param> + + </when> + <when value="single"> + <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="F">F</option> + <option value="R">R</option> + </param> + + </when> + </conditional> + + + </inputs> + <outputs> + <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/> + <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/> + + + </outputs> + <tests> + + + <test> + <param name="target" value="trinity/Trinity.fasta" /> + <param name="aligner" value="bowtie" /> + <param name="paired_or_single" value="single" /> + <param name="library_type" value="None" /> + <param name="input" value="trinity/reads.left.fq" /> + </test> + + + </tests> + <help> + .. _Trinity: http://trinityrnaseq.sourceforge.net + </help> +</tool>