Mercurial > repos > gkumar09 > trinityrnaseq_protocol
changeset 28:9b159468135f draft
Deleted selected files
| author | gkumar09 |
|---|---|
| date | Fri, 23 Oct 2015 12:07:53 -0400 |
| parents | 0bb2b5dc3a53 |
| children | f7c062297fb9 |
| files | trinityrnaseq_protocol/align_and_estimate_abundance.xml~ |
| diffstat | 1 files changed, 0 insertions(+), 89 deletions(-) [+] |
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--- a/trinityrnaseq_protocol/align_and_estimate_abundance.xml~ Fri Oct 23 12:07:36 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,89 +0,0 @@ -<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="transcript_file" value="fasta" /> - <param name="input" value="reads.left.fq" /> - <output name="transcripts_counts" value="text" /> - - </test> - - - </tests> - <help> - .. _Trinity: http://trinityrnaseq.sourceforge.net - </help> -</tool>